Database Summary Paper Alpha List

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1000 Genomes Selection Browser
Engelken, Johannes; Pybus, Marc; Dall'Olio, Giovanni; Luisi, Pierre; Uzkudun, Manu; CarreÃƒÂ±o-Torres, Angel; Pavlidis, Pavlos; Laayouni, Hafid; Bertranpetit, Jaume
Signature of selection in the human genomes
database
summary
2D-PAGE
Pleissner, K.-P., Eifert, T., Buettner, S., Knipper, J., Schmelzer, P., Stein, R., Schmidt, F., Mattow, J., Zimny-Arndt, U., Schmid, M., Jungblut, P.R.
Proteome database system for microbial research
database
summary
2P2Idb
Basse, MJ., Betzi, S., Bourgeas, R., Bouzidi, S., Chetrit, B., Hamon, V., Morelli, X., and Roche, P.
2P2Idb - database dedicated to the modulation of protein-protein interactions
database
summary
3D rRNA modification maps
Locations of modified rRNA nucleotides within the 3D structure of the ribosome
database
summary
3D-Footprint
Bruno Contreras-Moreira
Estimates of DNA-binding specificity for protein-DNA complexes in PDB
database
summary
3D-Interologs
Protein-protein interactions in various evolutionary lineages
database
summary
3DID - 3D interacting domains
Aloy, Patrick; Mosca, Roberto; Ceol, Arnaud; Stein, Amelie; Olivella, Roger
Domain-domain interactions in proteins with known 3D structures
database
summary
3DNALandscapes
Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, and Wilma K. Olson
Conformational features of DNA
database
summary
3DSNP
Lu, Yiming; Quan, Cheng; Ping, Jie; Lu, Hao; Zhou, Gangqiao
regulatory function of human noncoding variants by exploring their 3D interactions
database
summary
3DSNP
Zhang, Chenggang; Lu, Yiming; Quan, Chen; Chen, Hebing; Bo, Xiaochen
Regulatory roles of human noncoding SNPs: their 3D interactions with genes and other SNPs
database
summary
3DSwap: Database of Proteins involved in 3D domain Swapping
Khader Shameer
1,3
, Prasahant N. Shingate
, Manjunath, S.C.P.
, Karthika, M.
, Ganesan Pugalenthi
and Ramanathan Sowdhamini
1*
3DSwap, a database of domain swapped proteins
database
summary
4DXpress
Database for cross species expression pattern comparisons
database
summary
5S Ribosomal RNA Database
5S rRNA sequences
database
summary
Magnaporthe grisea
Database
Magnaporthe grisea
integrated physical/genetic map
database
summary
Medicago trunculata
Database
Medicago trunculata
-related resources
database
summary
Oryza
Tag Line
P. Larmande
, C. Gay
, C. Sallaud
, C. PÉrin
, P. Perez
, M. Lorieux
, J.B. Morel
, A.A.T. Johnson
, M. Ruiz
, B. Courtois
and E. Guiderdoni
T-DNA insertion mutants of rice
database
summary
Shi
Base
Yang J.
, Chen L.H.
, Yu J.
, Sun L.L.
, Jin Q.
Comparative genomics of
Shigella
database
summary
A3D Model Organism Database
Ventura, Salvador; Badaczewska-Dawid, Aleksandra; Kuriata, Aleksander; Pintado-Grima, Carlos; Garcia-Pardo, Javier; Burdukiewicz, MichaÅ‚; Iglesias, Valentin; Kmiecik, Sebastian
A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms
database
summary
AAgAtlas
Wang, Dan .; Yang, Liuhui; Zhang, Ping; Labaer, Joshua; Hermjakob, Henning; Li, Dong `; yu, xiaobo
Human autoantigen database
database
summary
AAgMarker
Qian, Jiang; Pan, Jianbo; Liu, Sheng; Zhu, Heng
No description supplied
database
summary
AAindex
Katayama, T., Kawashima, S., Kanehisa, M.
Physicochemical and biological properties of amino acids
database
summary
ABA - Ascidian Body Atlas
Hotta, K.
1,2
, Tahakashi, H.
, Ueno, N.
, Ikeo, K.
, Gojobori, T.
A digital 3D atlas of ascidian embryo development
database
summary
ABC Portal
Gao, Xin; Hong, Fang; Hu, Zhenyu; Zhang, Zilong; Lei, Yang; Li, Xiaoyun; Cheng, Tao,
Single cell transcriptomics of blood cells
database
summary
ABC-HuMi
Gurevich, Alexey; Hirsch, Pascal; Tagirdzhanov, Azat; Kushnareva, Aleksandra; Olkhovskii, Ilia; Graf, Simon; Schmartz, Georges; Mueller, Rolf; Keller, Andreas
ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome
database
summary
aBiofilm
Kumar, Manoj,; Rajput, Akanksha; Thakur, Anamika; Sharma, Shivangi
Biofilms play an important role in the antibiotic drug resistance, which is
database
summary
ABS
Blanco E.
1,2
, Farre D.
1,2
, Alba M.
, Messeguer X.
and Guigo R.
Experimentally verified orthologous transcription factor binding sites
database
summary
ACLAME - A Classification of Mobile genetic Elements
A classification of genetic mobile elements
database
summary
AcrDB
Yin, Yanbin; Huang, Le; Yang, Bowen; Yi, Haidong; Asif, Amina; Wang, Jiawei; Lithgow, Trevor; Zhang, Han; Minhas, Fayyaz-ul-Amir Afsar
anti-CRISPR operons
database
summary
AcrHub
Lithgow, Trevor; Wang, Jiawei; Dai, Wei; Li, Jiahui; Li, Qi; Xie, Ruopeng; Zhang, Yanju; Stubenrauch, Christopher
anti-CRISPR proteins
database
summary
ActiveDriverDB
Reimand, JÃƒÂ¼ri; Krassowski, Michal; Paczkowska, Marta; Cullion, Kim; Huang, Tina; Dzneladze, Irakli; Ouellette, Francis; Yamada, Joseph; Fradet-Turcotte, Amelie
No description supplied
database
summary
ACTIVITY
Functional DNA/RNA site activity
database
summary
ADC-DB
Zhu, Feng; Shen, Liteng; Sun, Xiuna; Chen, Zhen; Guo, Yu; Shen, Zheyuan; Song, Yi; Xin, Wenxiu; Ding, Haiying; Ma, Xinyue; Xu, Weiben; Zhou, Wanying; Che, Jinxin; Tan, Lili; Chen, Liangsheng; Chen, Siqi; Dong, Xiaowu; Fang, Luo
ADCdb: pharma-information and biological activity of antibody-drug conjugate
database
summary
ADDA - A Domain Database (Discontinued)
Andreas Heger and Liisa Holm
A database of protein domain families
database
summary
Addgene Repository Database
Kamens, Joanne
Plasmid vectors from publications and commercial sources
database
summary
ADHDgene
Wang Jing
Genetics of Attention Deficit Hyperactivity Disorder
database
summary
ADPriboDB
Leung, Anthony; Ayyappan, Vinay; Wat, Ricky; Barber, Calvin; Vivelo, Christina; Gauch, Kathryn; Visanpattanasin, Pat; Cook, Garth; Sazeides, Christos
ADP-ribosylated proteins and sites
database
summary
ADReCS
Ji, Zhi-Liang; Cai, Mei-Chun; Xu, Quan; Pan, Yan-Jing; Pan, Wen; Ji, Nan; Li, Yin-Bo; Jin, Hai-Jing; Liu, Ke
Adverse Drug Reaction Classification System
database
summary
ADReCS-Target
Ji, Zhi-Liang; Huang, Li-Hong; He, Qiu-Shun; Liu, Ke; Cheng, Jiao; Zhong, Min-Dong; Chen, Lin-Shan
No description supplied
database
summary
AFDB
Velankar, Sameer; Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna; Paramval, Urmila; Pidruchna, Ivanna; Radhakrishnan, Malarvizhi; Tsenkov, Maxim; Nair, Sreenath; Mirdita, Milot; Yeo, Jingi; Kovalevskiy, Oleg; Tunyasuvunakool, Kathryn; Å½Ãdek, Augustin; Hariharan, Dhavanthi; Abrahamson, Josh; Green, Tim; Jumper, John; Hassabis, Demis; Steinegger, Martin; Laydon, Agata; Birney, Ewan
AlphaFold Protein Structure Database in 2024: Providing structure coverage for over 214 million protein sequences
database
summary
AffinDB
Affinity data for protein-ligand complexes
database
summary
AgBase
McCarthy F.M.
1,2
, Bridges S.M.
2,3
, Wang N.
2,3
, Magee G.B.
2,3
, Williams W.P.
, Luthe D.
, and Burgess S.C.
1,3,6
GO annotations for agriculturally important plants and animals
database
summary
AGD -
Ashbya
Genome Database
Ashbya gossypii
genome database
database
summary
AgeAnno
Zhou, Xiaobo1; Huang, Kexin; Gong, Haoran; Guan, Jingjing; Zhang, Lingxiao; Hu, Changbao; Zhao, Weiling; Huang, Liyu; Zhang, Wei; Kim, Pora
Single cell annotation of aging in human
database
summary
AgeAnnoMO
Zhou, Xiaobo1 ; Huang, Kexin; Liu, Xi; Zhang, Zhaocan; Wang, Tiangang; Xu, Haixia; Li, Qingxuan; Jia, Yuhao; Kim, Pora; Huang, Liyu
AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging
database
summary
AgeFactDB
Suehnel, Juergen; Huehne, Rolf; Thalheim, Torsten
Ageing factors, phenotypes and lifespan data
database
summary
AGIDB
Li, Xinyun; Zhang, Kaili; Liang, Jiete; Fu, Yuhua; Chu, Jinyu; Fu, Liangliang; Wang, Yongfei; Li, Wangjiao; Zhou, You; Li, Jinhua; Yin, Xiaoxiao; Wang, Haiyan3; Liu, Xiaolei; Mou, Chunyan; Wang, Chong-Long; Wang, Heng; Dong, Xinxing; Yan, Dawei; Yu, Mei'; Zhao, Shuhong1; Ma, Yunlong
AGIDB: a versatile database for genotype imputation and variant decoding across species
database
summary
Aging Atlas
Liu, Guang-Hui
Aging related omics data
database
summary
AgingChart
Moskalev, Alexey; Zhikrivetskaya, Svetlana; Shaposhnikov, Mikhail; Dobrovolskaya, Eugenia; Gurinovich, Roman; Kuryan, Oleg; Pashuk, Aleksandr; Jellen, Leslie; Aliper, Alex; Peregudov, Alex; Zhavoronkov, Alex
Pathways of age-related processes
database
summary
AGRIS -
Arabidopsis
Gene Regulatory Information Server
Davuluri RV
, Sun H
, Palaniswamy SK
, Matthews N
, Molina C
, Grotewold E
Arabidopsis
gene regulatory information server: promoters, transcription factors and their target genes
database
summary
AHTPdb
Raghava, Gajender; Kumar, Ravi; Chaudhary, Kumardeep; Sharma, Minakshi; Nagpal, Gandharva; Chauhan, Jagat; Singh, Sandeep; Gautam, Ankur
Antihypertensive peptides database
database
summary
al MENA
Remya Koshy, Anop Ranawat, Vinod Scaria
al mena: a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations
database
summary
Allele Frequency Net
Gonzalez, Faviel; Takeshita, Louise; Melo Dos Santos, Eduardo; Kempson, Felicty; Maia, Maria Helena; Soares da Silva, Andrea; Teles e Silva, Andre; Ghattaoraya, Gurpreet; Alfirevic, Ana; Jones, Andrew; Middleton, Derek
Immunogenetic gene frequencies in worldwide populations
database
summary
Allen Brain Atlas
Susan Sunkin
Gene expression and neuroanatomical data.
database
summary
AlloMAPS
Zhen Wah Tan
, Wei-Ven Tee
1,2
, Enrico Guarnera
, Lauren Booth
1,3
and Igor N. Berezovsky
1,2,
AlloMAPS - allosteric mutation analysis and polymorphism of signaling database
database
summary
AlloMAPS
Tan, Zhen Wah; Tee, Wei-Ven; Guarnera, Enrico; Berezovsky, Igor
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta pre
database
summary
AlloMAPS: allosteric mutation analysis and polymorphism of signaling database
Tan, Zhen Wah;Tee, Wei-Ven;Guarnera, Enrico;Booth, Lauren;Berezovsky, Igor N
No description supplied
database
summary
Allosteric Database
Huang, Zhimin; Mou, Linkai; Shen, Qiancheng; Lu, Shaoyong; Liu, Xinyi; Wang, Guanqiao; Li, Shuai; Geng, Lv; Chen, Guoqiang; Zhang, Jian
Allosteric proteins and their activators, inhibitors, and regulators
database
summary
AlphaFold Protein Structure Database
Velankar, Sameer; Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna; Paramval, Urmila; Pidruchna, Ivanna; Radhakrishnan, Malarvizhi; Tsenkov, Maxim; Nair, Sreenath; Mirdita, Milot; Yeo, Jingi; Kovalevskiy, Oleg; Tunyasuvunakool, Kathryn; Å½Ãdek, Augustin; Hariharan, Dhavanthi; Abrahamson, Josh; Green, Tim; Jumper, John; Hassabis, Demis; Steinegger, Martin; Laydon, Agata; Birney, Ewan
AlphaFold Protein Structure Database in 2024: Providing structure coverage for over 214 million protein sequences
database
summary
ALPSbase
Autoimmune lymphoproliferative syndrome database
database
summary
AlterORF
Database of alternate open reading frames
database
summary
AlzGene
Bertram L.
, Mullin K.
, McQueen M.
, Blacker D.
, Tanzi R.E.
, Kinoshita J.
, Noyes P.
, Knep C.
A database of all published AlzheimerÃ¢â‚¬â„¢s disease genetic association studies
database
summary
AMDB
Chun, Jongsik; Yang, Junwon; Park, Jonghyun; Jung, Yeonjae
Animal Microbial Database
database
summary
AMIR
Qing-Yong Yang
Asteraceae Multi-omics Information Resource
database
summary
AmoebaDB
Functional Genomic Resource for Amoebazoa
database
summary
AMRnet
Kathryn Holt; et al.
AMRnet: A data visualisation platform to interactively explore pathogen variation
database
summary
AmtDB: a database of ancient human mitochondrial genomes
Ehler, Edvard;NovotnÃƒÂ½, JiÃ…â„¢ÃƒÂ;Juras, Anna;ChyleÃ…â€žski, Maciej;MoravÃ„\x8DÃƒÂk, OndÃ…â„¢ej;PaÃ„\x8Des, Jan
No description supplied
database
summary
Amylograph
Burdukiewicz, MichaÅ‚; Rafacz, Dominik; Barbach, Agnieszka; Hubicka, Katarzyna; BÄ…kaÅ‚a, Laura; Lassota, Anna; Stecko, Jakub; SzymaÅ„ska, Natalia; Wojciechowski, Jakub; Kozakiewicz, Dominika; Szulc, Natalia; Chilimoniuk, JarosÅ‚aw; JÄ™Å›kowiak, Izabela; GÄ…sior-
Amyloid-amyloid interactions
database
summary
AmyPro
Pancsa, Rita; Varadi, Mihaly; De Baets, Greet; Vranken, Wim; Tompa, Peter
No description supplied
database
summary
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
Huang, Xiaosong;Albou, Laurent-Philippe;Mushayahama, Tremayne;Muruganujan, Anushya;Tang, Haiming;Thomas, Paul D
No description supplied
database
summary
Animal Genome Size Database
Gregory, T.R.
Genome sizes of vertebrates and invertebrates
database
summary
Animal QTLdb and CorrDB
Hu, Zhi-Liang; Park, Carissa; Reecy, James
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenge
database
summary
Animal Toxin Database
Database of animal toxins
database
summary
Animal-APAdb
Gong, Jing; Jin, Weiwei; Zhu, Qizhao; Yang, Yanbo; Yang, Wenqian; Wang, Dongyang.; Yang, Jiajun; Niu, Xiaohui; Yu, Debing
Alternative polyadenylation in animals
database
summary
Animal-eRNAdb
Gong, Jing; Jin, Weiwei; Jiang, Guanghui; Yang, Yanbo; Yang, Jianye; Yang, Wenqian; Wang, Dongyang.; Niu, Xiaohui; Zhong, Rong; Zhang, Zhao
Animal enhancer RNAs
database
summary
Animal-SNPAtlas
Gong, Jing; Gao, Yingjie; Jiang, Guanghui; Yang, Wenqian; Jin, Weiwei; Xu, Xuewen; Niu, Xiaohui
High-quality SNPs in 20 animal species
database
summary
AnimalMetaOmics
Hu, Shengwei; Hu, Ruirui; Li, Fulin; Chen, Yifan; Liu, Chuyang; Li, Jiawei; Ma, Zhongchen; Wang, Yue; Cui, Chaowen; Luo, Chengfang; Zhou, Ping1; ni, wei; Yang, Qing-Yong
AMLdb: a multi-omics data resources for exploring animal microbial genomes and microbiomes
database
summary
AnimalQTLdb
Z.-L. Hu, E.R. Fritz and J.M. Reecy
Quantitative trait loci in livestock animals
database
summary
AnimalTFDB
Guo, Anyuan; Shen, Wen-Kang; Chen, Siyi; Gan, Zi-Quan; Zhang, Yu-Zhu; Yue, Tao; Chen, Miao-Miao; Xue, Yu; Hu, Hui
AnimalTFDB 4.0: a comprehensive animal transcription factor database update
database
summary
AnimalTFDB
Guo, An-Yuan; Zhang, Hong-Mei.; Liu, Teng; Liu, Chun-Jie; Song, Shuangyang; Zhang, Xiantong; Liu, Wei.; Jia, Haibo; Xue, Yu
Animal Transcription Factor Database
database
summary
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors
Hu, Hui;Miao, Ya-Ru;Jia, Long-Hao;Yu, Qing-Yang;Zhang, Qiong;Guo, An-Yuan
No description supplied
database
summary
ANISEED
Lemaire, Patrick; Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Nitta, Kazuhiro; Naville, Magali; Piette, Jacques; Scornavacca, CÃƒÂ©line; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Besnardeau, Lydia; Fagotto, Marie; GuÃƒÂ©roult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Mendez, Mickael; Reeves, Wendy; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, FrÃƒÂ©dÃƒÂ©ric; Douzery, Emmanuel; Dumollard, RÃƒÂ©mi; Kusakabe, Takehiro; Nakai, Kenta; NISHIDA, Hiroki; Satou, Yutaka; Veeman, Michael; Volff, Jean-Nicolas
No description supplied
database
summary
ANISEED
Lemaire, Patrick; Brozovic, Matija; Martin, Cyril; Dantec, Christelle; Dauga, Delphine; Mendez, Mickael; Simion, Paul; Percher, Madeline; Laporte, Baptiste; Scornavacca, CÃƒÂ©line; Fujiwara, Shigeki; Gineste, Mathieu; Lowe, Elijah; Piette, Jacques; Sasakura, Yasunori; Takatori, Naohito; Brown, Titus; Delsuc, Frederic; Gissi, Carmela; DOUZERY, Emmanuel; McDougall, Alex; NISHIDA, Hiroki; Sawada, Hitoshi; Swalla, Billie; Yasuo, Hitoyoshi
No description supplied
database
summary
ANPDB
Stefan Gunther; et al.
African Natural Products Database (ANPDB): A Resource for Exploring the Chemical Diversity of African Biodiversity
database
summary
anti-CRISPRdb
Guo, Feng-Biao; Dong, Chuan; Hao, Ge-Fei; Hua, Hong-Li; Liu, Shuo; Labena, Abraham; Chai, Guoshi; Huang, Jian.,; Rao, Nini
Anti-CRISPRdb is a comprehensive online resource that effectively organizes
database
summary
Antibody Registry
Bandrowski, Anita; Pairish, Mason; Eckman, Peter; Grethe, Jeffrey; Martone, Maryann
Antibodies, their antigens and catalogue numbers
database
summary
AntigenDB
Hifzur Rahman Ansari, Darren R. Flower, and G.P.S. Raghava
Sequence, structure, and other data on pathogen antigens
database
summary
AntiJen
Toseland C.P., Clayton D.J., McSparron H., Hemsley S.L., Blythe M.J., Paine K., Doytchinova I.A., Guan P., Hattotuwagama C.K. and Flower D.R.
Quantitative binding data for peptides and proteins of immunological interest
database
summary
antiSMASH
Weber, Tilmann; Blin, Kai; Shaw, Simon; Kautsar, Satria; Medema, Marnix
antibiotics and Secondary Metabolite Analysis SHell
database
summary
antiSMASH database
Blin, Kai; Weber, Tilmann; Shaw, Simon; Medema, Marnix
The antiSMASH database version 4: Additional genomes and BGCs, new sequence-based searches, and more.
database
summary
APAatlas: decoding alternative polyadenylation across human tissues
Hong, Wei;Ruan, Hang;Zhang, Zhao;Ye, Youqiong;Liu, Yaoming;Li, Shengli;Jing, Ying;Zhang, Huiwen;Diao, Lixia;Liang, Han;Han, Leng
Alternative polyadenylation (APA) is an RNA-processing mechanism on the 3Ã¢
database
summary
APASdb
You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Tian, Peng; Chen, Liangfu; Li, Yuxing; Luan, Yijie; Huang, Guangrui; Chen, Chengyong; Huang, Shengfeng; Chen, Shangwu; Xu, Anlong
Alternative poly(A) sites and downstream cleavage sites
database
summary
APD - Antimicrobial Peptide Database
Antimicrobial peptide database
database
summary
AphidBase
Genomic database for the pea aphid (
Acyrthosiphon pisum
database
summary
ApiDB - Apicomplexan DataBase
Aurrecoechea C.
, Heiges M.
, Wang H.
, Wang Z.
, Fischer S.
, Rhodes P.
,Miller J.
, Kraemer E.
, Stoeckert C.
, Roos D.
, Kissinger J.
1,5
Unified resource for various apicomplexan species
database
summary
ApiDots
EST sequences from various apicomplexan parasites
database
summary
ApoHoloDB
Tien-Hao Chang
Apo- and Holo- structure pairs of proteins
database
summary
AppaDB
A database on the nematode
Pristionchus pacificus
database
summary
APPRIS
Tress, Michael; RodrÃƒÂguez, Jose; Rodriguez-Rivas, Juan; Di Domenico, Tomas; Vazquez, Jesus; Valenica, Alfonso
No description supplied
database
summary
APPRIS
Michael Tress
A system for annotating alternative splice isoforms
database
summary
APPRIS
Tress, Michael; RodrÃguez, Jose; Pozo, Fernando; CerdÃ¡n-VÃ©lez, Daniel; di Domenico, Tomas; Vazquez, Jesus
APPRIS: selecting functionally important isoforms
database
summary
Aquila
Cheung, Edwin; Zheng, Yimin; chen, yitian; Ding, Xianting; Wong, Chris Koon Ho
Spatial omics data
database
summary
Arabidopsis Hormone Database
Peng, Z.Y.
, Zhou, X.
, Li, L.
, Yu, X.
, Li, H.
, Jiang, Z.
, Cao, G.
, Bai, M.
, Wang, X.
, Jiang, C
, Lu, H.
, Hou, X.
, Qu, L
, Wang, Z.
, Zuo, J.
, Fu, X.
, Su, Z.
, Li, S.
, and Guo, H.
A Comprehensive Genetic and Phenotypic Information Database for Plant Hormone Research in Arabidopsis
database
summary
Arabidopsis Mitochondrial Protein Database
Heazlewood J.L., Tonti-Filippini J.S., Gout A., Day D.A., Whelan J. and Millar A.H.
Experimentally identified mitochondrial proteins in
Arabidopsis
database
summary
Arabidopsis MPSS
Arabidopsis
gene expression detected by massively parallel signature sequencing
database
summary
Arabidopsis Nucleolar Protein Database
Comparative analysis of nucleolar proteomes of human and
Arabidopsis
database
summary
ArachnoServer
Volker Herzig, David L. A. Wood, Felicity Newell, Pierre-Alain Chaumeil, Quentin Kaas, Greta J. Binford, Graham M. Nicholson, Dominique Gorse, and Glenn F. King
Sequence, structure and activity of protein toxins from spider venom
database
summary
AraGWAS Catalog
Korte, Arthur; Togninalli, Matteo; Seren, ÃƒÅ“mit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef; Borgwardt, Karsten; Grimm, Dominik
No description supplied
database
summary
ARAMEMNON
Schwacke, R.
, Schneider, A.
, van der Graaff, E.
, Desimone, M.
, Frommer, W.B.
2,3
, FlÜgge, U.I.
, Kunze, R.
Arabidopsis thaliana membrane proteins and transporters
database
summary
AraNet
Lee, Insuk; Lee, Tak; Yang, Sunmo; Kim, Eiru; Ko, Younhee; Hwang, Sohyun; Shin, Junha; Shim, Jung; Shim, Hongsuk; Kim, Hyojin; Kim, Chanyoung
Functional relationships between plant genes
database
summary
AraPheno
Korte, Arthur; Seren, ÃƒÅ“mit; Grimm, Dominik; Fitz, Joffrey; Weigel, Detlef; Nordborg, Magnus; Borgwardt, Karsten
Phenotypic data for Arabidopsis thaliana
database
summary
Araport
Krishnakumar, Vivek; Hanlon, Matthew; Contrino, Sergio; Ferlanti, Erik; Karamycheva, Svetlana; Kim, Maria; Rosen, Benjamin; Cheng, Chia-Yi; Moreira, Walter; Mock, Stephen; Stubbs, Joseph; Sullivan, Julie; Krampis, Konstantinos; Miller, Jason; Micklem, Gos; Vaughn, Matthew; Town, Christopher
Arabidopsis Information Portal established by the International Arabidopsis Informatics Consortium
database
summary
ArchDB
Bonet J, Planas-Iglesias J, Garcia-Garcia J, MarÃƒÂn-LÃƒÂ³pez MA, Fernandez-Fuentes N, Oliva B.
Automated classification of protein loop structures
database
summary
ARDB
Liu, B.
, Pop, M.
1,2
Antibiotic resistance genes in bacteria
database
summary
ARED
Bakheet, T.
, Williams, B.
, Khabar, K.
AU-rich element-containing mRNAs
database
summary
ARED-Plus
Khabar, Khalid; Bakheet, Tala; Hitti, Edward
No description supplied
database
summary
AREsite
Andreas R. Gruber, JÃƒÆ’Ã‚Â¶rg Fallmann, Franz Kratochvill, Pavel Kovarik, and Ivo L. Hofacker
AU-rich elements in vertebrate mRNA UTR sequences
database
summary
ARKbase
Anshu Bhardwaj; et al.
ARKbase: Antimicrobial Resistance Knowledgebase 1.0
database
summary
ArrayMap
Cai, Haoyang; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael Baudis
Gene copy number profiling data in human cancer
database
summary
ARTS-DB
Ziemert, Nadine; Mungan, Mehmet; Blin, Kai
Database for Antibiotic Resistant Targets
database
summary
AS-ALPS
Alternative Splicing-induced Alteration of Protein Structure
database
summary
ASAP - A Systematic Annotation Package
Community analysis of
E. coli
and related genomes
database
summary
ASC - Active Sequence Collection
Angelo Facchiano
, Antonio Facchiano
, Francesco Facchiano
Biologically-active short amino acid sequences
database
summary
ASCancer
Wu, Song; Huang, Yue; Zhang, Mochen; Gong, Zheng; Guoliang, Wang; Zheng, Xinchang; Wenting, Zong; Zhao, Wei; Xing, Peiqi; Li, Rujiao; Liu, Zhaoqi; Bao, Yi-Ming
Alternative splicing in cancer
database
summary
ASD
Zhang, Jian#; He, Jixiao; Liu, Xinyi.; Zhu, Chunhao; Zha, Jinyin; Li, Qian; Zhao, Mingzhu; Wei, Jiacheng; Li, Mingyu; Wu, Chengwei; Wang, Junyuan; Jiao, Yonglai; Ning, Shaobo; Zhou, Jiamin; Hong, Yue; Liu, Yonghui; He, Hongxi; Zhang, Mingyang; Chen, Feiying; Li, Yanxiu; Song, Kun; Lu, Xuefeng
ASD2023: towards the integrating landscapes of allosteric knowledgebase
database
summary
ASMdb
Li, Guoliang; Zhou, Qiangwei; Guan, Pengpeng; Zhu, Zhixian; Cheng, Sheng; Zhou, Cong; Wang, Huanhuan; Xu, Qian; Sung, Wing- Kin
Allele-Specific DNA Methylation Database
database
summary
ASPD
Valuev, V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A.
Artificial Selected Proteins/Peptides Database
database
summary
ASpdb
Pora Kim
Structures of human protein isoforms
database
summary
ASpedia
Park, Charny; Hyoung, Daejin; Cho, Soo Young
No description supplied
database
summary
Aspergillus Genomes
Unified Aspergillus resource with medical and genomic data
database
summary
AspGD
Cerqueira, Gustavo; Arnaud, Martha; Inglis, Diane; Skrzypek, Marek; Binkley, Jonathan; Orvis, Joshua,; Shah, Prachi; Wymore, Farrell; Sherlock, Gavin; Wortman, Jennifer
The
Aspergillus
Genome Database
database
summary
ASPicDB
Alternative Splicing Prediction DataBase
database
summary
ASRP - Arabidopsis Small RNA Project
Arabidopsis thaliana small RNA project
database
summary
ASTRA
Antonis Giannakakis; et al.
ASTRA: A Comprehensive Resource of Stress-Induced Transcriptional Activation
database
summary
ATACdb
Li, Chunquan; Wang, Fan,; Bai, Xuefeng; Wang, Yuezhu; Jiang, Yong'; Ai, Bo; Liu, Yuejuan; Xu, Mingcong; Wang, Qiuyu; Han, Xiaole; Pan, QI; Li, Yanyu; Li, Xuecang; Zhang, Jian.,; Zhao, Jun; Feng, Chenchen; Zhu, Jiang',
Human Assay-for-Transposase-Accessible Chromatin data
database
summary
ATGC
David M. Kristensen
, Yuri I. Wolf
and Eugene Koonin
Alignable Tight Genomic Clusters of Closely Related Prokaryotic Genomes
database
summary
AtGDB
Schlueter, S.D.
, Wilkerson, M.D.
, Brendel, V.
1,2
Arabidopsis thaliana genome database
database
summary
AthaMap
Genome-wide map of putative transcription factor binding sites in
Arabidopsis thaliana
database
summary
ATLAS
Gelly, Jean-Christophe; Vander Meersche, Yann; Cretin, Gabriel; Gheeraert, Aria; Galochkina, Tatiana
ATLAS: protein flexibility description from atomistic molecular dynamics simulations
database
summary
AtMAD
Shi, Tieliu; Lan, Yiheng; Sun, Ruikun; Ouyang, Jian; Ding, Wubin; Kim, Min-Jun; Li, Yuhua
Arabidopsis thaliana Multi-omics Association Database
database
summary
AtPID
Arabidopsis thaliana Protein Interactome Database
database
summary
ATTED-II
Obayashi T.
1,2,3
, Kinoshita K.
4,5
, Nakai K.
, Shibaoka M.
, Hayashi S.
, Saeki M.
, Shibata D.
, Saito K.
2,3,8
and Ohta H.
1,9
Coexpressed gene sets and gene regulators in
Arabidopsis
database
summary
AutDB
Catalog of genes linked to Autism Spectrum Disorders
database
summary
AutDB
Banerjee-Basu, Sharmila; Pereanu, Wayne; Larsen, Eric; Das, Ishita.; EstÃƒÂ©vez, Marcel; Sarkar, Anjali; Pearson, Senanu; Kollu, Ravi; Basu, Saumyendra
AutDB is a deeply annotated resource for exploring the impact of genetic va
database
summary
AutismKB
Liping Wei
Autism genetics KnowledgeBase
database
summary
Autophagy Database
Hui Liu, Wei Liu, Yifang Liao, Long Cheng, Qian Liu, Xiang Ren, Lisong Shi, Xin Tu, Qing Kenneth Wang, and An-Yuan Guo
Proteins involved in self-digestion of eukaryotic cells
database
summary
AutoPSI
Automated structural classification of protein sequences
database
summary
autoSNPdb
Plant SNP discovery database
database
summary
AVPdb
Qureshi, Abid; Thakur, Nishant; Tandon, Himani; Kumar, Manoj
A database of experimentally validated AntiViral Peptides
database
summary
Bac
Dive
Reimer, Lorenz; SardÃ Carbasse, Joaquim; Koblitz, Julia; Ebeling, Christian; Podstawka, Adam; Overmann, JÃ¶rg
Bac
Dive
the knowledge base for standardized bacterial and archaeal d
database
summary
BacDive
SÃƒÂ¶hngen, Carola; Podstawka, Adam; Bunk, Boyke; Gleim, Dorothea; Vetcininova, Anna; Reimer, Lorenz; Ebeling, Christian; Pendarovski, Cezar; Overmann, JÃƒÂ¶rg
Bacterial Diversity metadatabase
database
summary
BacMap
Wishart, David; Cruz, Joseph; Liu, Yifeng; Liang, Jack; Zhu, You; Wilson, Michael.; Dennis, Jonathan; Stothard, Paul; Van Domselaar, Gary
Picture atlas of annotated bacterial genomes
database
summary
BacMet
Pal, C.
, Bengtsson-Palme, J.
, Rensing, C.
, Kristiansson, E.
, Larsson, DGJ.
Antibacterial Biocide and Metal Resistance Genes
database
summary
Bacterial CSDB (BCSDB)
Bacterial Carbohydrate Structure DataBase
database
summary
Bacteriome.org
Protein interaction database for E. coli
database
summary
BACTIBASE
Bacteriocin natural antimicrobial peptides
database
summary
BacWGSTdb
Ruan, Zhi; Feng, Ye; Zou, Shengmei; Chen, Hangfei; Yu, Yunsong
Bacterial whole genome sequence typing database
database
summary
BAliBASE
Benchmark database for comparison of multiple sequence alignments
database
summary
BAR
Nicholas Provart
Bio-Analytic Resource for Plant Biology
database
summary
BARCdb
Galli, Joakim; Oelrich, Johan; Taussig, Michael; Andreasson, Ulrika; Ortega-Paino, Eva; Landegren, Ulf
Biobanking Analysis Resource Catalogue
database
summary
BARD
Howe, Eleanor; de Souza, Andrea; Lahr, David; Chatwin, Simon; Montgomery, Philip; Alexander, Benjamin; Nguyen, Dac-Trung; Cruz, Yasel; Stonich, Derek; Walzer, Gil; Rose, Jason; Picard, Shaita; Liu, Zihan; Rose, Jaime; Xiang, Xiaorong; Asiedu, Jacob; Durkin, Daniel; Levine, Jeri; Yang, Jeremy; Schurer, Stephan; Braisted, Johnathan; Southall, Noel; Southern, Mark; Chung, Thomas; Brudz, Stephen; Tanega, Cordelle; Schreiber, Stuart L; Bittker, Joshua; Guha, Rajarshi; Clemons, Paul
BioAssay Research Database
database
summary
BarleyBase
Shen L.
, Gong J.
1,5
, Xin J.
1,5
, Caldo R.A.
, Nettleton D.
, Cook D.
, Wise R.P.
2,4
and Dickerson J.A.
1,5
Expression profiling of plant genomes
database
summary
BastionHub
Lithgow, Trevor; Wang, Jiawei; Li, Jiahui; Hou, Yi; Dai, Wei; Xie, Ruopeng; Marquez-Lago, Tatiana; Leier, Andre; Zhou, Tieli; Torres, Von; Hay, Iain; Stubenrauch, Christopher; Zhang, Yanju; Song, Jiangning
Substrates of Gram-negative secretion systems
database
summary
BATMAN-TCM
Li, Dong; Kong, Xiangren; Liu, Chao; Zhang, Zuzhen; Mei, Zhijun; Li, Xiangdong; Cheng, Meiqi; Liu, Peng; Diao, Lihong; Ma, Yajie; Jiang, Peng; Kong, Xiangya; Nie, Shiyan; Guo, Yingzi; Wang, Ze; Zhang, Xinlei; Wang, Yan; Guo, Shuzhen; Liu, Zhongyang
BATMAN-TCM 2.0: an enhanced integrative database for known and predicted linkages between traditional Chinese medicine ingredients and target proteins
database
summary
BCCTBbp
Chelala, Claude; Cutts, Rosalind; Guerra, Afonso; Gadaleta, Emanuela; Dayem Ullah, Abu
Breast Cancer Campaign Tissue Bank bioinformatics portal
database
summary
BCIpep
Saha S., Bhasin M. and Raghava G.P.S.
A database of B-cell epitopes
database
summary
BCNTB bioinformatics
Chelala, Claude; Gadaleta, Emanuela; PirrÃƒÂ², Stefano; Dayem Ullah, Abu; Marzec, Jacek
No description supplied
database
summary
BeetleBase
Genome database of the beetle
Tribolium castaneum
database
summary
Benchmark
Sonego P., Pacurar M., Dhir S., Farkas A.T., Kocsor A., GÃƒÂ¡spÃƒÂ¡ri Z., Leunissen J.A.M. and Pongor S.
Protein classification benchmark collection: training/test sets for machine learning
database
summary
BetAware
Savojardo C., Fariselli P., Casadio R.
Subcellular localization of entire eukaryotic proteomes
database
summary
BFVD
Martin Steinegger
AlphaFold-predicted structures of viral proteins [CHECK]
database
summary
BGC Atlas
Caner Bagci
Biosynthetic gene clusters from metagenomes
database
summary
Bgee
Frederic B Bastian, Alessandro Brandulas Cammarata, Sara Carsanaro, Harald Detering, Wan-Ting Huang, Sagane Joye, Anne Niknejad, Marion Nyamari, Tarcisio Mendes de Farias, SÃ©bastien Moretti, Marianna Tzivanopoulou, Julien Wollbrett, Marc Robinson-Rechavi
Gene expression patterns across species
database
summary
BGI-RISe - Beijing Genomics Institute Rice Information System
Zhao W.
, Wang J.
, He X.
, Huang X.
, Jiao Y.
, Dai M.
, Wei S.
, Fu J.
, Chen Y.
, Ren X.
, Zhang Y.
1,2
, Ni P.
, Zhang J.
, Li S.
1,2
, Wang J.
, Wong G.K.-S.
1,3
, Zhao H.
, Yu J.
, Yang H.
and Wang J.
Integrated rice database
database
summary
BGMUT
Olga Blumenfeld
Blood Group Antigen Gene Mutation Database
database
summary
BIC
JUAN, HSUEH-FEN; Chen, Kai-Pu; Hsu, Chia-Lang; Oyang, Yen-Jen; Huang, Hsuan-Cheng
Bacteria in Cancer
database
summary
BiG-FAM
Medema, Marnix; Kautsar, Satria; Blin, Kai; Shaw, Simon; Weber, Tilmann
Biosynthetic gene cluster families
database
summary
BiGG Models
Lewis, Nathan; King, Zachary; Lu, Justin; DrÃƒÂ¤ger, Andreas; Miller, Philip; Federowicz, Steve; Lerman, Joshua; Ebrahim, Ali; Palsson, Bernhard
Biochemically, Genetically and Genomically structured metabolic networks
database
summary
BIGNASim
GelpÃƒÂ, Josep LluÃƒÂs; Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo; Battistini, Federica; Torres, Jordi; GoÃƒÂ±i, Ramon; Orozco, Modesto
Molecular dynamics simulations of Nucleic Acids
database
summary
Binding MOAD
Ahmed, Aqeel; Smith, Richard; Clark, Jordan; Dunbar, Jim; Carlson, H.A.
Binding Mother of All Databases: a database of protein-ligand crystal structures
database
summary
BindingDB
Liu T., Lin Y., Wen X., Jorissen R.N. and Gilson M.K.
Binding affinities of protein-ligand and other complexes
database
summary
BioCyc
A collection of hundreds of databases that integrate genome and metabolic pathway data.
database
summary
BioDrugScreen
Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, and Samy O. Meroueh
A resource for computational drug design and discovery
database
summary
BioExcel-CV19 [CHECK]
Hospital, Adam; BeltrÃ¡n, Daniel; GelpÃ, Josep LluÃs; Orozco, Modesto
A New paradigm for Molecular Dynamics Databases: The Covid19 database, the legacy of a titanic community effort
database
summary
BioFuelDB
Chaudhary N, Gupta A, Gupta S, Sharma VK.
In light of the rapid decrease in fossils fuel reserves and an increasing d
database
summary
BioGPS
Andrew I. Su
Gene annotation portal and a resource on gene and protein function
database
summary
BioGRID
Tyers, Mike; Chatr Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heineke, Sven; Boucher, Lorrie; Chen, Daici; Stark, Chris; Breitkreutz, Ashton; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Nixon, Julie; Ramage, Lindsay; Winter, Andrew; Sellam, Adnane; Chang, Christie; Hirschman, Jodi; Theesfeld, Chandra; Rust, Jennifer; Livstone, Mike; Oughtred, Rose; Dolinski, Kara
Genetic and physical interactions in yeast, worm and fly
database
summary
BioKA
Zhao, Wen-Ming; Wang, Yibo; Lin, Yihao; Wu, Sicheng; Sun, Jiani; Meng, Yuyan; Jin, Enhui; Kong, Demian; Duan, Guangya; Bei, Shaoqi; Fan, Zhuojing; Wu, Gangaoinactive; Hao, Lili; Song, Shuhui; Tang, Bi-Xia
BioKA: A curated and integrated biomarker knowledgebase for Animals
database
summary
BioLiP
Jianyi Yang
Biologically relevant ligand-protein interactions
database
summary
BioLIP
Zhang, Chengxin; Zhang, Xi; Freddolino, Peter; Zhang, Yang,
BioLiP2: a structure database for biological relevant ligand-protein interactions
database
summary
BioMagResBank
Markley, J., Ulrich, E.
NMR spectroscopic data from proteins, peptides, and nucleic acids
database
summary
Biomodels
Malik-Sheriff, Rahuman; Glont, Mihai; Nguyen, Tung; Graesslin, Martin; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala; Kothamachu, Varun; Rodriguez, Nicolas; Swat, Maciej; Eils, JÃƒÂ¼rgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi; Le Novere, Nicolas; Hermjakob, Henning
BioModels serves as a central repository of mathematical models representin
database
summary
BioModels
Juty, Nick; Chelliah, Vijayalakshmi; Ajmera, Ishan; Ali, Raza; Dumousseau, Marine; Glont, Mihai; Hucka, Mike; Jalowicki, GaÃƒÂ«l; Keating, Sarah; Knight-Schrijver, Vincent; Lloret Villas, Audald; Natarajan, Kedar; Pettit, Jean-Baptiste; Rodriguez, Nicolas; Schubert, Michael; Wimalaratne, Sarala; Zhou, Yangyang; Hermjakob, Henning; Le Novere, Nicolas; Laibe, Camille
Published mathematical models of biological interest
database
summary
BioMuta and BioExpress
Kahsay, Robel; Dingerdissen, Hayley; Torcivia, John; Hu, Yu; Chang, Ting-Chia; Mazumder, Raja
No description supplied
database
summary
Bionemo
Curated information about biodegradation-related genes and proteins
database
summary
BioNumbers
Ron Milo, Paul Jorgensen, Uri Moran, Griffin Weber, and Michael Springer
Useful biological numbers
database
summary
BioSamples
Gupta, Dipayan; Liyanage, Isuru; Perez-Riverol, Yasset; Sapena Ventura, Enrique; Kheng Teh, Wei; Van Den Bossche, Tim; Vijayaraja, Senthilnathan; Khen, Amnon; Sarkans, Ugis; Burdett, Tony; Rajan, Jeena
Biological samples used as sources of sequence, structure or expression data
database
summary
BioSamples
Courtot, MÃ©lanie; Liyanage, Isuru; Xu, Fuqi; Gupta, Dipayan; Burdett, Tony
BioSamples database: FAIRer samples metadata to accelerate research data ma
database
summary
BioSilico
Integrated access to various metabolic databases
database
summary
BioStudies
Ugis Sarkans, Anja FÃƒÂ¼llgrabe, Ahmed Ali, Awais Athar, Ehsan Behrangi, Nestor Diaz, Silvie Fexova, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Rada, Irene Papatheodorou, Brazma, Alvis
BioStudies database
database
summary
BioStudies
Sarkans, Ugis; Gostev, Mikhail; Athar, Awais; Behrangi, Ehsan; Melnichuk, Olga; Ali, Ahmed; Minguet, Jasmine; Rada, Juan; Snow, Catherine; Tikhonov, Andrew; Brazma, Alvis; McEntyre, Johanna
No description supplied
database
summary
BioThesaurus
Liu H.
, Hu Z.Z.
and Wu C.H.
A collection of gene/protein names and associated sequences
database
summary
BIOZON
Yona G., Birkland A.
A system for unification and analysis of heterogeneous biological data
database
summary
BISC
Thomas Juettemann
1,2
and Dietlind L. Gerloff
Binary SubComplexes in Proteins Database
database
summary
BitterDB
Masha Niv
Bitter taste: molecules and receptors
database
summary
BloodChIP
Pimanda, John; Thoms, Julie; Koch, Forrest; Raei, Alireza; Subramanian, Shruthi; Wong, Jason; Vafaee,
Transcription factor binding profiles in human haematopoietic stem/progenitor cells
database
summary
BloodChIP
Pimanda, John; Thoms, Julie; Koch, Forrest; Raei, Alireza; Subramanian, Shruthi; Wong, Jason; Vafaee, Fatemeh
BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells
database
summary
BloodExpress
Database of Gene Expression in Mouse Haematopoiesis
database
summary
BloodSpot
Bagger, Frederik; GÃslason, MagnÃºs; Demircan, GÃ¼l; Prachar, Marek; FurtwÃ¤ngler, Benjamin; Schwaller, Jurg; Schoof, Erwin M.; Porse, Bo; Rapin, Nicolas
BloodSpot 3.0
database
summary
BloodSpot
Frederik Otzen Bagger
BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis
database
summary
BMRB
Hoch, Jeffrey; Baskaran, Kumaran; Burr, Harrison; Chin, John; Eghbalnia, Hamid R.; Fujiwara, Toshimichi; Gryk, Michael; Iwata, Takeshi; Kojima, Chojiro; Kurisu, Genji; Maziuk, Dmitri; Miyanoiri, Yohei; Wedell, Jonathan R.; Wilburn, Colin; Yao, Hongyang; Y
Biological Magnetic Resonance Data Bank
database
summary
bNAber
Godzik, Adam; Eroshkin, Alexey; LeBlanc, Andrew; Weekes, Dana; Post, Kai; Li, Zhanwen; Rajput, Akhil; Butera, Sal; Burton, Dennis
A database of broadly neutralizing HIV-1 antibodies
database
summary
BodyParts3D
Database of human anatomy, represented as 3D anatomical concepts
database
summary
Bovine Genome
Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, C. Michael Dickens, Kevin L. Childs, Hanni Salih, Anna K. Bennett, Darren E. Hagen, David L. Adelson, and Christine G. Elsik
Bovine Genome Database
database
summary
BPS
Database of RNA Base-Pair Structures
database
summary
BRAD
Wang, Xiaowu; Chen, Haixu; Wang, Tianpeng; He, Xiaoning; Cai, Xu; Lin, Runmao; Liang, Jianli; Wu, Jian; King, Graham J
Brassica Database
database
summary
Brain Catalog
Pan, Siyu; Hongen, Kang; Liu, Xinxuan; Lin, Shiqi; è‹‘, å¨œ; Zhang, Zhang; Bao, Yi-Ming; Jia, Peilin
Genetics of brain disorders and related phenotypes
database
summary
BrainBase
Zhang, Zhang; Liu, Lin; Zhang, Yang; Niu, Guangyi; Li, Qianpeng; Li, Zhao; Zhu, Tongtong; Feng, Changrui; Liu, Xiaonan; Zhang, Yuansheng; Xu, Tianyi; Chen, Ruru; Teng, Xufei; Zhang, Rongqin; Zou, Dong; Ma, Lina
Brain disease knowledgebase
database
summary
BrainScope
Dongsheng Chen; et al.
BrainScope: cross-species multi-dimensional brain atlas
database
summary
Brassica Genome
T.A. Erwin
1,2,3
, E.G. Jewell
1,2
, C.G. Love
1,2
, G.A.C. Lim
1,2
, Xi Li
1,2
, R. Chapman
, J. Batley
, J. Stajich
, E. Mongin
1,5
, E. Stupka
, B. Ross
, G. Spangenberg
1,2,3
and D. Edwards
1,2,3
A database for
Brassica
genomic research
database
summary
BreCAN-DB
Chowdhury, Shantanu; Narang, Pankaj; Dhapola, Parashar
Breakpoint profiles of CANcer genomes
database
summary
BRENDA
Schomburg, Dietmar; Chang, Antje; Jeske, Lisa; Ulbrich, Sandra; Hofmann, Julia; Koblitz, Julia; Schomburg, Ida; Neumann-Schaal, Meina; Jahn, Dieter
Enzyme names and biochemical properties
database
summary
Brix
Peter Vanhee
1,2
, Erik Verschueren
, Lies Baeten
1,2
, Francois Stricher
, Luis Serrano
3,4
, Frederic Rousseau
1,2
and Joost Schymkowitz
1,2
Protein building blocks for structural analysis, modeling and design
database
summary
BSDB
Mateusz Sikora
, Joanna I. Sułkowska
, Bartłomiej S. Witkowski
and Marek Cieplak
Biomolecule Stretching Database
database
summary
BSORF -
Bacillus subtilis
Open Reading Frames
Bacillus subtilis genome database at Kyoto U.
database
summary
BSRD
Lei Li, Dandan Huang, Man Kit Cheung, Wenyan Nong, Qianli Huang and Hoi Shan Kwan
A repository of bacterial small regulatory RNA
database
summary
BTO
Marion Gremse
, Antje Chang
, Ida Schomburg
, Andreas Grote
, Maurice Scheer
, Christian Ebeling
and Dietmar Schomburg
BRENDA Tissue Ontology
database
summary
BuchneraBase
Genome of the pea aphid symbiont
Buchnera
sp. APS
database
summary
BV-BRC
Davis, James; Olson, Robert; Assaf, Rida; Brettin, Thomas,; Conrad, Neal; Cucinell, Clark; Dempsey, Donald; Dickerman, Allan; Dietrich, Emily; Kenyon, Ronald; Kuscuoglu, Mehmet; Lefkowitz, Elliot; Lu, Jian; Machi, Dustin; Macken, Catherine; Mao, Chunhong;
Bacterial and Viral Bioinformatics Resource Center
database
summary
BYKdb
Christophe Combet
Bacterial protein tYrosine Kinase database
database
summary
BÂµG@Sbase
Adam Witney
Microarray datasets for microbial gene expression
database
summary
CADB - Conformational Angles DataBase of Proteins
Sheik, S.S., Ananthalakshmi, P., Ramya Bhargavi, G., Sekar, K.
Conformation angles of protein structures, with associated crystallographic data
database
summary
CADD
Kircher, Martin; Schubach, Max; Maass, Thorben; Nazaretyan, Lusine
CADD v1.7: Using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions
database
summary
CADgene
Hui Liu, Wei Liu, Yifang Liao, Long Cheng, Qian Liu, Xiang Ren, Lisong Shi, Xin Tu, Qing Kenneth Wang, and An-Yuan Guo
Coronary Artery Disease gene database
database
summary
CADRE - Central Aspergillus Data Repository
Mabey Gilsenan, Jane; Cooley, John; Bowyer, Paul
Central Aspergillus data repository
database
summary
CaeNDR
Andersen, Erik; Crombie, Timothy; McKeown, Ryan; Moya, Nicolas; Evans, Kathryn; Widmayer, Samuel; LaGrassa, Vincent; Roman, Natalie; Tursunova, Orzu; Zhang, Gaotian; Gibson, Sophia; Buchanan, Claire; Roberto, Nicole; Vieira, Rodolfo; Tanny, Robyn
CaeNDR, the Caenorhabditis Natural Diversity Resource
database
summary
CAGE
Kawaji H.
, Kasukawa T.
1,2
, Fukuda S.
, Katayama S.
, Kai C.
, Kawai J.
2,3
, Carninci P.
2,3
, and Hayashizaki Y.
2,3
CAGE tags for cap-analysis of gene expression
database
summary
CAGm: a repository of germline microsatellite variations in the 1000 genomes project
Kinney, Nicholas;Titus-Glover, Kyle;Wren, Jonathan D;Varghese, Robin T;Michalak, Pawel;Liao, Han;Anandakrishnan, Ramu;Pulenthiran, Arichanah;Kang, Lin;Garner, Harold R
No description supplied
database
summary
CAMERA
Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel Lin, Steve Peltier, Karen Stocks, Eric E. Allen, Mark Ellisman, Jeffrey Grethe, and John Wooley
Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis of metagenomic data
database
summary
CAMP
Idicula-Thomas, Susan; Gawde, Ulka; Chakraborty, Shuvechha; Waghu, Faiza; Barai, Ram; Khanderkar, Ashlesha; Indraguru, Rishikesh; Shirsat, Tanmay
CAMPR4: A database of natural and synthetic antimicrobial peptides
database
summary
CAMP
Idicula-Thomas, Susan; Waghu, Faiza; Gopi, Lijin; Barai, Ram Shankar; Ramteke, Pranay; Nizami, Bilal
Collection of Anti-Microbial Peptides
database
summary
Cancer RNA-Seq Nexus
Liu, Chun-Chi; Li, Jian-Rong; Sun, Chuan-Hu; Li, Wenyuan,; Chao, Rou-Fang; Huang, Chieh-Chen; Zhou, X. Jasmine
No description supplied
database
summary
Cancer3D
Godzik, Adam; Porta Pardo, Eduard; Hrabe, Thomas
Mapping of cancer mutations to protein structures
database
summary
CancerGenes
Higgins ME, Claremont M, Major JE, Sander C, Lash AE
A gene selection resource for cancer genome projects
database
summary
CancerImmunityQTL
Miao, Xiaoping (proxy) (contact); Tian, Jianbo; Cai, Yimin; Li, Yue; Lu, Zequn; Huang, Jinyu; Deng, Yao; Yang, Nan'; Wang, Xiaoyang; Ying, Pingting; Zhang, Shanshan; Zhu, Ying.; Zhang, Huilan; Zhong, Rong; Chang, Jiang
immunQTLs across multiple cancer types
database
summary
CancerMIRNome
Li, Ruidong; Qu, Han; Wang, Shibo; Chater, John; Wang, Xuesong; Cui, Yanru; Yu, Lei; Zhou, Rui; Jia, Qiong; Traband, Ryan; Wang, Meiyue; Xie, Weibo; Yuan, Dongbo; Zhu, Jianguo; Zhong, Weide; Jia, Zhenyu,
miRNA profiles in cancer
database
summary
CancerPPD
Raghava, Gajender; Tyagi, Atul; Tuknait, Abhishek; Anand, Priya; Gupta, Sudheer; Sharma, Minakshi; Mathur, Deepika; Joshi, Anshika; Singh, Sandeep; Gautam, Ankur
Experimentally validated anticancer peptides
database
summary
CancerProteome
Li, Yongsheng; Lv, Dezhong; Li, Donghao; Cai, Yangyang; Guo, Jiyu; Chu, Sen; Yu, Jiaxin; Liu, Kefan; Jiang, Tiantongfei; Ding, Na; Jin, Xiyun; Xu, Juan
CancerProteome: a resource for functionally deciphering proteome landscape in cancer
database
summary
CancerResource
Jessica Ahmed
, Thomas Meinel
, Mathias Dunkel
, Manuela S. Murgueitio
, Robert Adams
, Corinna Blasse
, Andreas Eckert
, Saskia Preissner
and Robert Preissner
Cancer-relevant proteins and compound interactions
database
summary
CancerSCEM
Xiao, Jingfa; Zeng, Jingyao; Zhang, Yadong.; Shang, Yunfei; Mai, Jialin; Shi, Shuo; Lu, Mingming; Bu, Congfan; Zhang, Zhewen; Zhang, Zaichao; Li, Yang; Du, Zhenglin1
Human cancer single-cell gene expression
database
summary
CandidaDB
C. dÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢Enfert
, S. Goyard
, S. Rodriguez-Arnaveilhe
, L. Frangeul
, L. Jones
, F. Tekaia
, O. Bader
, A. Albrecht
, L. Castillo
, A. Dominguez
, J. Ernst
, C. Fradin
, C. Gaillardin
, S. Garcia-Sanchez
, P. de Groot
10
, B. Hube
, F.M. Klis
10
, S. Krishnamurthy
, D. Kunze
, M.-C. Lopez
, A. Mavor
11
, N. Martin
, I. Moszer
, D. OnÉsime
, J. Perez Martin
12
, R. Sentandreu
, E. Valentin
and A.J.P. Brown
11
Candida albicans
genome database
database
summary
Candidate Cancer Gene Database
Starr, Timothy; Abbott, Kenneth; Nyre, Erik; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel
Cancer genes identified in transposon-based forward genetic screens in mice
database
summary
CanGEM
Gene copy number changes in cancer
database
summary
canSAR
Al-Lazikani, Bissan; DiMicco, Patrizio; Antolin, Albert; Mitsopoulos, Costas; Villasclaras Fernandez, Eloy; Sanfelice, Domenico; Dolciami, Daniela; Ramagiri, Pradeep; Mica, John; Tym, Joe; Gingrich, Philip; Hu, Huabin; Workman, P.
canSAR: update to the cancer translational research and drug discovery knowledgebase
database
summary
CanSAR
Al-Lazikani, Bissan; Mitsopoulos, Costas; DiMicco, Patrizio; Villasclaras Fernandez, Eloy; Dolciami, Daniela; Holt, Esty; Mica, Iona; Coker, Elizabeth; Tym, Joe; Campbell, James; Che, Ka Hing; Ozer, Bugra; Kannas, Christos; Antolin, Albert; Workman, P.
Integrated cancer research and drug discovery resource
database
summary
CAPS-DB
Narcis Fernandez-Fuentes
Classification of helix cappings in protein structures
database
summary
Carbohydrate Structure Database (CSDB)
Toukach, Philip; Egorova, Ksenia
Carbohydrate Structure Database
database
summary
CARD
McArthur, Andrew; Jia, Baofeng; Raphenya, Amogelang; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara; Lago, Briony; Dave, Biren; Pereira, Sheldon; Sharma, Arjun; Doshi, Sachin; Courtot, MÃƒÂ©lanie; Lo, Raymond; Williams, Laura; Frye, Jonathan; Elsayegh, Tariq; Sardar, Daim; Westman, Erin; Pawlowski, Andrew; Johnson, Timothy; Brinkman, Fiona; Wright, Gerard D.
Comprehensive Antibiotic Research Database
database
summary
CARD
Alcock, Brian; Huynh, William; Chalil, Romeo; Smith, Keaton; Raphenya, Amogelang; Wlodarski, Mateusz; Edalatmand, Arman; Petkau, Aaron; Syed, Sohaib; Tsang, Kara; Baker, Sheridan; Dave, Mugdha; McCarthy, Madeline; Mukiri, Karyn; Nasir, Jalees; Golbon, Bah
CARD 2023: Expanded Curation, Support for Machine Learning, and Resistome P
database
summary
CarpeDB
Locke, C.J., Caldwell, K.A., Caldwell, G.A.
A database on the genetics of epilepsy
database
summary
CaSNP
Qingyi Cao, Meng Zhou, Xujun Wang, Cliff A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, and X. Shirley Liu
Cancer SNP data on copy number alterations
database
summary
CASpedia
Doudna, Jennifer A; Adler, Benjamin; Trinidad, Marena; Bellieny-Rabelo, Daniel; Zhang, Elaine; Karp, Hannah; Skopintsev, Petr; Thornton, Brittney; Weissman, Rachel; Yoon, Peter; Chen, LinXing; Hessler, Tomas; Eggers, Amy; Colognori, David; Boger, Ron; Doherty, Erin; Tsuchida, Connor; Tran, Ryan; Hofman, Laura; Shi, Honglue; Wasko, Kevin M.; Zhou, Zehan; Xia, Chenglong; Al-Shimary, Muntathar; Patel, Jaymin R.; Thomas, Vienna; Pattali, Rithu; Kan, Matthew; Vardapetyan, Anna; Yang, Alana; Lahiri, Arushi; Maxwell, Michaela; Murdock, Andrew; Ramit, Glenn; Henderson, Hope; Calvert, Roland W.; Bamert, Rebecca S.; Knott, Gavin; Lapinaite, Audrone; Pausch, Patrick; Cofsky, Joshua; Sontheimer, Erik; Wiedenheft, Blake; Fineran, Peter; Brouns, Stan; Sashital, Dipali; Thomas, Brian; Brown, Christopher; Goltsman, Daniela S. A.; Barrangou, Rodolphe; Siksnys, Virginijus; Banfield, Jillian; Savage, David
CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes
database
summary
CATH
Sillitoe, Ian; Bordin, Nicola; Dawson, Natalie; Waman, Vaishali; Ashford, Paul; Scholes, Harry; Pang, Camilla; Rauer, Clemens; Woodridge, Laurel; Sen, Neeladri; Abbasian, Mahnaz; Le Cornu, Sean; Lam, Su Datt; Berka, Karel; HutaÃ…â„¢ovÃƒÂ¡ VaÃ…â„¢ekovÃƒÂ¡, Ivana; Svobodova, Radka; Lees, Jonathan; Orengo, Christine
Protein domain structures database
database
summary
CATMA - Complete Arabidopsis Transcriptome MicroArray
Arabidopsis gene sequence tags
database
summary
CauloBrowser
Lasker, Keren; Schrader, Jared; Men, Yifei; Marshik, Tyler; Dill, David; McAdams, Harley; Shapiro, Lucy
Cell cycle program of Caulobacter crescentus
database
summary
CAZy
Terrapon, Nicolas; Drula, Elodie; Garron, Marie-Line; Dogan, Suzan; Lombard, Vincent; Henrissat, Bernard
Carbohydrate-Active Enzymes database
database
summary
CAZy
Henrissat, Bernard; Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie; Coutinho, Pedro M.
Carbohydrate-Active Enzymes database
database
summary
cBioPortal
Nikolaus Schultz, Chris Sander, Jianjiong Gao, BÃƒÂ¼lent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, Gideon Dresdner, Rileen Sinha, Yichao Sun, Caitlin J. Byrne, Michael L. Heuer, Yevgeniy Antipin, Boris Reva, Arthur P. Goldberg, S. Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson, Ethan Cerami,
The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
database
summary
CC+
A resource for elucidating sequence-to-structure relationships for coiled-coil folding and assembly
database
summary
CCCDb
Chunquan Li; et al.
CCCDb: A comprehensive manually curated database for Cell-Cell Communication
database
summary
CCDB
Subhash M. Agarwal, Dhwani Raghav, Harinder Singh, and G.P.S. Raghava
Cervical cancer gene database
database
summary
CCDB - The CyberCell Database
E. coli
database at U. Alberta
database
summary
CCDS
Pruitt, Kim; Farrell, Catherine; O'Leary, Nuala; Harte, Rachel; Loveland, Jane; Wilming, Laurens; Wallin, Craig; Diekhans, Mark; Barrell, Daniel; Searle, Stephen; Aken, Bronwen; Hiatt, Susan; Frankish, Adam; Suner, Marie-Marthe; Rajput, Bhanu; Steward, Charles; Brown, Garth; Bennett, Ruth; Murphy, Michael; Wu, Wendy; Kay, Mike; Hart, Jennifer; Rajan, Jeena; Weber, Janet; Snow, Catherine; Riddick, Lillian; Hunt, Toby; Webb, David; Tamez, Pamela; Rangwala, Sanjida; McGarvey, Kelly; Mudge, Jonathan; Pujar, Shashikant; Shkeda, Andrei; Mudge, Jonathan; Gonzalez, Jose; Gilbert, James G. R.; Trevanion, Stephen; Baertsch, Robert; Harrow, Jennifer; Ostell, James; Haussler, David; Hubbard, Tim
Consensus set of annotated full-length human protein-coding regions
database
summary
CCDS
Murphy, Terence; Pujar, Shashikant; O'Leary, Nuala; Farrell, Catherine; Loveland, Jane; Mudge, Jonathan M.; Wallin, Craig; GarcÃƒÂa GirÃƒÂ³n, Carlos; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew.; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike; Kodali, Vamsi; MacÃƒÂas, JosÃƒÂ©; Martin, Fergal; McAndrews, Monica; McGarvey, Kelly; Murphy, Michael,,; Rajput, Bhanu; Rangwala, Sanjida; Riddick, Lillian; Seal, Ruth; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen; Bruford, Elspeth; Bult, Carol; Frankish, Adam; Pruitt, Kim
Consensus coding sequence database
database
summary
ccmGDB
Zhao, Zhongming; Kim, Pora; Cheng, Feixiong; Zhao, Junfei
Cancer Cell Metabolism Gene Database
database
summary
ccNET
Su, Zhen; You, Qi; Xu, Wenying; Zhang, Kang; Zhang, Liwei; Yi, Xin; Yao, Dongxia; Wang, Chunchao; Zhang, Xueyan; Zhao, Xinhua; Provart, Nicholas; Li, Fuguang
Co-expression networks for diploid and polyploid Gossypium
database
summary
ccPDB
Gajendra Raghava
Compilation and Creation of datasets from Protein Data Bank
database
summary
CCSD - Complex Carbohydrate Structure Database (CarbBank)
Complex carbohydrate structure database
database
summary
CD-CODE
Ksenia Kuznetsova
1,2
, Maxim Scheremetjew
1,2
, Jialin Yin
1,2
, HongKee Moon
1,2
, Diego A. Vargas
, Anna Hadarovich
1,2
, Natasha Lewis
1,2
, Carsten Hoege
1,2
, Chi Fung Willis Chow
1,2
, David Kuster
1,2
, Jik Nijssen
1,2
, Alberto Hernandez-Armendariz
1,3
, Jonathan C. Savage
1,2
, Yu Wei
1,2
, Silja Zedlitz
1,2,5
, Hari Raj Singh
1,2
, Soumyadeep Ghosh
1,2
, Allysa P Kemraj
6,7
, Lena Hersemann
1,2
, Anthony A. Hyman
1,2,5
, Diana Mitrea
, Agnes Toth-Petroczy
1,2,3
CrowDsourcing COndensate Database and Encyclopedia
database
summary
CDD
Marchler-Bauer, Aron; Derbyshire, Myra; Gonzales, Noreen; Lu, Shennan; Chitsaz, Farideh; Geer, Lewis; Geer, Renata; He, Jane; Gwadz, Marc; Hurwitz, David; Lanczycki, Christopher; Lu, Fu; Marchler, Gabriele; Song, James; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne; Zhang, Dachuan; Zheng, Chanjuan; Bryant, Steve
Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases
database
summary
CDD/SPARCLE
Marchler-Bauer, Aron; Wang, Jiyao; Chitsaz, Farideh; Derbyshire, Myra; Gonzales, Noreen; Gwadz, Marc; Lu, Shennan; Marchler, Gabriele; Song, James; Thanki, Narmada; Yamashita, Roxanne; Yang, Mingzhang; Zhang, Dachuan,; Zheng, Chanjuan; Lanczycki, Christop
The Conserved Domain Database in 2023
database
summary
CDD/SPARCLE: the conserved domain database in 2020
Lu, Shennan;Wang, Jiyao;Chitsaz, Farideh;Derbyshire, Myra K;Geer, Renata C;Gonzales, Noreen R;Gwadz, Marc;Hurwitz, David I;Marchler, Gabriele H;Song, James S;Thanki, Narmada;Yamashita, Roxanne A;Yang, Mingzhang;Zhang, Dachuan;Zheng, Chanjuan;Lanczycki, Christopher J;Marchler-Bauer, Aron
No description supplied
database
summary
CDS-DB
Liu, Zhongyang; Chen, Ruzhen; Yang, Lele; Jiang, Jianzhou; Ma, Shurui; He, Mengqi; Mao, Yichao; Guo, Congcong; Kong, Xiangya; Zhang, Xinlei; Qi, Yaning; Li, Dong
CDS-DB, an omnibus for patient-derived gene expression signatures induced by cancer treatment
database
summary
CEBS
Fostel, Jennifer; Martini, Cari; Liu, Ying; Gong, Hui.; Sayers, Nicole; Segura, German
CEBS update: curated toxicology database with enhanced tools for data integ
database
summary
CEBS
Database of toxicogenomics, microarray and proteomics data
database
summary
CeCaFDB
Xie, Xiaoyao; Liu, Zhijie; Shen, Tie; Wen, Han; Yi, Yin; Zhang, Zhengdong; Zhou, Xiangfei; Zhou, Wenwei; Shang, Chuanyu; Liu, Xiaoguang; Xin, Chenwei; Li, Gang; Jiang, Jiansi; Li, Chao; Rui, Bin; Yu, Guojun; Han, Mengshu; Li, Ruiyuan; You, Shanping
Carbon flux data of central metabolism in various organisms
database
summary
CEDAR
KoÅŸaloÄŸluâ€\x90YalÃ§Ä±n, Zeynep; Blazeska, Nina; Vita, Randi; carter, hannah; Nielsen, Morten; Schoenberger, Stephen; Sette, Alex; Peters, Bjoern,
Cancer Epitope Database and Analysis Resouce
database
summary
CeDR
Jia, Peilin; Wang, Yin-Ying; Hongen, Kang; Xu, Tianyi; Hao, Lili; Bao, Yi-Ming
Drug responses in health and disease from scRNA-seq
database
summary
CEGA
Zdobnov, Evgeny; Dousse, Aline; Junier, Thomas
Conserved Elements from Genomic Alignments
database
summary
Cell Image Library
David Orloff
Images, videos, and animations of various cell types from diverse organisms
database
summary
Cell Taxonomy
Zhang, Zhang; Jiang, Shuai; Qian, Qiheng; Zhu, Tongtong; Zong, Wenting; Shang, Yunfei; Jin, Tong; Zhang, Yuansheng; Chen, Ming; Wu, Zishan; Chu, Yuan; Zhang, Rongqin; Luo, Sicheng; Jing, Wei; Zou, Dong; Bao, Yi-Ming; Xiao, Jingfa
Cell types and markers across species, tissues and conditions
database
summary
Cell Tracer
Guo, Qiuyan.; Wang, Peng; Liu, Qian; Hao, Yangyang2; Gao, Yue; Qi, Yue; Xu, Rongji; Chen, Hongyan; Xin, Mengyu; Wu, Xiaoting; Sun, Rui; Zhi, Hui1; zhang, Yunpeng`; Ning, Shangwei; Li, Xia
Multi-omics of cellular development trajectories
database
summary
CellCircuits
Mak H.C.
, Daly M.
, Gruebel B.
and Ideker T.
Molecular network models: from pairwise molecular interactions to whole pathways
database
summary
CellCommuNet
Pan, Jianbo; Ma, Qinfeng; Li, Qiang; Zheng, Xiao
CellCommuNet: an atlas of cellâ€“cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states
database
summary
CellFinder
Kurtz, Andreas; Stachelscheid, Harald; Seltmann, Stefanie; Lekschas, Fritz; Fontaine, Jean; Mah, Nancy; Neves, Mariana; Andrade-Navarro, Miguel; Leser, Ulf
Gene and protein expression, phenotype and images mapped to the cell types
database
summary
CellLineNavigator
Markus Krupp
A compendium of cell line expression profiles by microarray analysis
database
summary
CellMarker
Hu, Congxue; Li, Tengyue; Xu, Yingqi; Zhang, Xinxin; Li, Feng'.; Bai, Jing..; Chen, Jing; Jiang, Wenqi; Yang, Kaiyue; Ou, Qi; Li, Xia; Wang, Peng; zhang, Yunpeng`
CellMarker 2.0: an updated database of manually curated cell markers in hum
database
summary
CellMinerCDB
Fathi Elloumi , William C Reinhold , Sudhir Varma , Yanghsin Wang , Meric Kinali , Yasuhiro Arakawa , Yoshitaka Inoue , Mirit I Aladjem , Yves Pommier , Augustin Luna
CellMiner Cross-Database (CellMinerCDB) Version 2.2 for Explorations of Drug and Molecular Profiles in Cancer Cell Lines
database
summary
CellSNVReg
Tingting Shao; et al.
CellSNVReg: a multi-dimensional resource for SNV-mediated regulatory perturbations in single cells
database
summary
CellSTAR
Yang, Qingxia; Zhang, Ying; Sun, Huaicheng; Zhang, Wei; HUANG, Shijie; Mou, Minjie; Zhang, Jinsong; Gao, Jianqing; Ge, Yichao; Zhu, Feng
CellSTAR: a comprehensive single-cell transcriptomic annotation resource
database
summary
CELLxGENE
Bailey Marshall
Curated, standardized single-cell transcriptomic data
database
summary
CeNDR
Andersen, Erik; Cook, Daniel; Zdraljevic, Stefan; Roberts, Joshua
C. elegans Natural Diversity Resource
database
summary
CentrosomeDB
Alves-Cruzeiro, J., Nogales-Cadenas, R., Pascual-Montano, A.
Human centrosomal proteins database
database
summary
Cereal Small RNA Database
Small RNAs expressed in rice and maize
database
summary
CFam
C. Zhang, L. Tao, C. Qin, P. Zhang, S.Y. Chen, X. Zeng, F. Xu, Z. Chen, S.Y. Yang
Similarity-based classification of chemical compounds
database
summary
CFEA: a cell-free epigenome atlas in human diseases
Yu, Fulong;Li, Kai;Li, Shuangquan;Liu, Jiaqi;Zhang, Yan;Zhou, Meng;Zhao, Hengqiang;Chen, Hongyan;Wu, Nan;Liu, Zhihua;Su, Jianzhong
Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcy
database
summary
CFGP
Lee, Yong-Hwan; Choi, Jaeyoung; Cheong, Kyeongchae; Jung, Kyongyong; Jeon, Jongbum; Lee, Gir-Won; Kang, Seogchan; Kim, Sangsoo; Lee, Yin-Won
Comparative Fungal Genomics Platform
database
summary
cfOmics
Lu, Zhi; Li, Mingyang; Zhou, Tianxiu; Han, Mingfei; Wang, Hongke; Bao, Pengfei; Tao, Yuhuan; Chen, Xiaoqing; Wu, Guansheng; Liu, Tianyou; Wang, Xiaojuan; Lu, Qian; Zhu, Yunping
cfOmics: A Cell-Free Multi-Omics Database for Diseases
database
summary
CGD - Candida Genome Database
Marek S. Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R. Miyasato, Matt Simison, and Gavin Sherlock
Candida albicans
genome database
database
summary
CGDB
Xue, Yu; Li, Shujing; Shui, Ke; Zhang, Ying.; Lv, Yongqiang; Ullah, Shahid; Deng, Wankun; Zhang, Luoying
Circadian Gene database
database
summary
ChannelsDB
Koca, Jaroslav; Pravda, LukÃƒÂ¡Ã…Â¡; Sehnal, David; SvobodovÃƒÂ¡ VarekovÃƒÂ¡, Radka; NavrÃƒÂ¡tilovÃƒÂ¡, Veronika; TouÃ…Â¡ek, Dominik; Berka, Karel; Otyepka, Michal
No description supplied
database
summary
ChannelsDB
Berka, Karel ; Å paÄ\x8DkovÃ¡, Anna; VÃ¡vra, OndÅ™ej; RaÄ\x8Dek, TomÃ¡Å¡; Sehnal, David; SvobodovÃ¡, Radka; Bednar, David; Damborsky, Jiri; Bazgier, Vaclav
ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era
database
summary
CharProtDB
Ramana Madupu
Experimentally Characterized Protein annotations
database
summary
ChEBI - Chemical Entities of Biological Interest
O'Boyle, Noel; Malik, Adnan; Arsalan, Muhammad; Moreno, Carlos; Mosquera, Juan; Felix, Eloy; KizilÃ¶ren, Tevfik; Muthukrishnan, Venkatesh; Zdrazil, Barbara; Leach, Andrew R
Small molecules, atoms, ions and radicals of biological interest
database
summary
Chem(Pro)2 NB superscript
Qingxia Yang
Chemoproteomic probes labelling human proteins
database
summary
ChemBank
Ferraiolo P.
, Bodycombe N.E.
, Brudz S.E.
, Clemons P.A.
, Eliasof S.
, George G.A.
, Happ M.P.
, Harris, E.
, Lach A.D.
, Muhlich, J.L.
, Seiler K.P.
, Selfors L.M.
, Serrano M.A.
, Sullivan J.P.
, Sulthan N.B.
, Tevelev, A.
, Tolliday N.
and Schreiber S.L.
1,2
Structures and biological activities of small organic molecules
database
summary
ChEMBL
Zdrazil, Barbara; Felix, Eloy; Hunter, Fiona; Manners, Emma; Blackshaw, James; Corbett, Sybilla; De Veij, Marleen; Ioannidis, Harris; Mendez, David; Mosquera, Juan; MagariÃ±os, Maria Paula; Bosc, Nicolas; Arcila, Ricardo; KizilÃ¶ren, Tevfik; Gaulton, Anna; Bento, A. Patricia; Adasme, Melissa; Monecke, Peter; Landrum, Gregory; Leach, Andrew R
Interaction of drugs and compounds with their targets
database
summary
ChemDB
Chen J.H., Swamidass S.J., Dou Y., Linstead E. and Baldi P.
3D structures and properties of small molecules
database
summary
ChemFOnt
Wishart, David; Jovel, Juan; Budinsky, Zachary; Oler, Eponine; Peters, Harrison; Milford, Ralph; Liu, Vicki; Sayeeda, Zinat; Mah, Robert; Wei, William S; Badran, Hasan; Lo, Elvis; Yamamoto, Mai; Djoumbou-Feunang, Yannick; Karu, Naama; Gautam, Vasuk
Chemical Functional Ontology
database
summary
Chemical Probes Portal
Antolin, Albert; Sanfelice, Domenico; Crisp, Alisa; Villasclaras Fernandez, Eloy; Mica, Iona; Chen, Yi; Collins, Ian; EDWARDS, Aled; MÃ¼ller, Susanne; Al-Lazikani, Bissan; Workman, P.
Chemical probe assessment and selection
database
summary
ChemPert
del Sol, Antonio; Zheng, Menglin; Okawa, Satoshi; Bravo, Miren; Chen, Fei; MartÃnez-Chantar, MarÃa
Transcriptomics responses to pertubagens in non-cancerous cells
database
summary
ChemProt
Olivier Taboureau
, Sonny Kim Nielsen
, Karine Audouze
, Nils Weinhold
, Daniel Edsga„rd
, Francisco S. Roque
, Irene Kouskoumvekaki
, Alina Bora
, Ramona Curpan
, Thomas Skøt Jensen
, Søren Brunak
and Tudor I. Oprea
1,3
Disease Chemical Biology Database
database
summary
Chewie-NS
Ramirez, MÃƒÂ¡rio; Mamede, Rafael; Vila-Cerqueira, Pedro; Silva, Mickael; Carrico, Joao
Gene-by-gene schemas for microbial strain identification
database
summary
ChickenGTEx Atlas
Zhang, Yali; et al.
The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping traits in chicken
database
summary
ChickVD
Wang J.
, He X.
2,3
, Ruan J.
2,3
, Dai M.
, Chen J.
, Zhang Y.
1,2
, Hu Y.
, Ye C.
, Li S.
, Cong L.
, Fang L.
, Liu B.
, Li S.
1,2
, Wang J.
, Burt D.W.
, Wong G.K.-S.
2,5
, Yu J.
2,6
, Yang H.
2,6
and Wang J.
1,2,7,8
Sequence variation in the chicken genome
database
summary
ChimerDB
Kim N.
, Kim P.
, Nam S.
, Shin S.
and Lee S.
Chimeric (fusion) sequences in human, rat and mouse
database
summary
ChIPBase
Liang-Hu Qu
Decoding transcriptional regulation of lncRNA and microRNA genes from ChIP-Seq data
database
summary
ChIPBase
Yang, Jian-Hua; Huang, Junhong; Zheng, Wujian; Zhang, Ping; Lin, Qiao; Chen, Zhirong; Xuan, Jiajia; Liu, Chang; Wu, Di; Huang, Qiaojuan; Zheng, Lingling; Liu, Shurong; Zhou, Ke-Ren; Qu, Liang-Hu; Li, Bin
ChIPBase v3.0: The Encyclopedia of Transcriptional Regulations of Non-codin
database
summary
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
Kurtenbach, Stefan;Reddy, Rohit;Harbour, JÃ‚Â William
No description supplied
database
summary
ChiTaRS
Milana Frenkel-Morgenstern
Human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
database
summary
ChlamDB
Trestan Pillonel, Florian Tagini, Claire Bertelli and Gilbert Greub
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum
database
summary
Chloroplast Genome Database
Cui L., Veeraraghavan N., Richter A., Wall K., Jansen R.K., Leebens-Mack J., Makalowska I. and dePamphilis C.W.
Chloroplast genome database
database
summary
ChromDB
Chromatin-associated proteins in a broad range of organisms
database
summary
ChromLoops
Zhou, Qiangwei; Cheng, Sheng; Zheng, Shanshan; Wang, Zhenji; Guan, Pengpeng; Zhu, Zhixian; Huang, Xingyu; Zhou, Cong1; Li, Guoliang
Protein-mediated chromatin loops
database
summary
ChromPolymerDB
Konstantinos Chronis; et al.
ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Polymers
database
summary
Ciliate IES-MDS database
Macro- and micronuclear genes in spirotrichous ciliates
database
summary
CIPRO
Endo, T.
An integrated protein database of the ascidian
Ciona intestinalis
database
summary
CircaDB
Angel Pizarro
A database of circadian expression profiles
database
summary
CircaKB
Zhiwei Ji
Circadian Genes
database
summary
circAtlas
Zhao, Fangqing; Wu, Wanying; Zhang, Jinyang
No description supplied
database
summary
CircleBase
Mao, Fengbiao; zhao, xiaolu; Shi, Leisheng; Ruan, Shasha; Bi, Wenjian; Li, Mingkun.; Qiao, Jie`
Human extrachromosomal circular DNA
database
summary
circMine
Zhang, Wenliang; Liu, Yang; Min, Zhuochao; Liang, Guodong; Mo, Jing; Ju, Zhen; Zeng, Binghui,; Guan, Wen; Zhang, Yan; Chen, Jianliang; Zhang, Qianshen; Li, Hanguang; Zeng, Chunxia; Wei, Yanjie; Chan, Godfrey Chi Fung
Human circRNA transcriptome in health and diease
database
summary
CircNet
Huang, Hsien-Da; Liu, Yu-Chen; Li, Jian-Rong; Sun, Chuan-Hu; Andrews, Erik; Chao, Rou-Fang; Lin, Feng-Mao; Weng, Shun-Long; Hsu, Sheng-Da; Huang, Chieh-Chen; Cheng, Chao; Liu, Chun-Chi
Tissue-specific circRNA expression profiles and regulatory networks
database
summary
CircNet
Huang, Hsien-Da; Chen, Yigang; Yao, Lantian; Tang, Yun; Jhong, Chase; Wan, Jingting; Chang, Jingyue; Cui, Shidong; Luo, Yijun; Cai, Xiaoxuan; Li, Wenshuo; Chen, Qi; Huang, Hsi-Yuan; Wang, Zhuo; Chen, Weiming; Chang, Tzu-Hao; Wei, Fengxian; Lee, Tzong-Yi
CircNet 2.0: an updated database for exploring circular RNA regulatory netw
database
summary
circRNADisease
Jiang, Tao; Sun, Zhi-Yan; Yang, Chang-Lin; Huang, Lijie; Mo, Zong-Chao; Zhang, Ke-Nan; Fan, Wen-Hua; Wang, Kuan-Yu; Wu, Fan`; Wang, Jiguang; Meng, Lin; Zhao, Zheng
CircRNADisease v2.0: an updated resource for high-quality experimentally supported circRNA-disease associations
database
summary
CircTarget
Xue, Yuanchao; Zhang, Hongmei; Zhang, Yuyang; Li, Peng; Yuan, Zhen; Liu, Wanglong; Zhang, Jinyue; Li, Ruitian; Lu, Chen; Zhu, Ping
CircTarget: an integrated resource for circRNA-target gene interactions and regulatory networks
database
summary
CirGRDB
Sun, zhongsheng; Li, Xianfeng; Shi, Leisheng; Zhang, Kun; Wei, Wenqing; Liu, Qi' ,; Mao, Fengbiao; Li, Jinchen; Cai, Wanshi; Chen, Huiqian; Teng, Huajing; Li, Jia-Da
No description supplied
database
summary
cisRED
Robertson A.G.
, Bilenky M.
, Lin K.
, He A.
, Yuen, W.
, Dagpinar M.
, Varhol R.
, Teague K.
, Griffith O.L.
, Zhang X.
, Pan, Y.
, Hassel M.
, Sleumer M.C.
, Pan, W.
, Pleasance E.D.
, Chuang, M.
, Hao H.
, Li Y.Y.
, Robertson N.
, Fjell C.
, Li B.
, Montgomery S.B.
, Astakhova T.
, Zhou J.
, Sander J.
, Siddiqui A.S.
and Jones S.J.M.
Phylogenetically conserved regulatory DNA sequence motifs
database
summary
Cistrome Data Browser
Meyer, Clifford; Taing, Len; Dandawate, Ariaki; L'Yi, Sehi; Gehlenborg, Nils; Brown, Myles
Cistrome Data Browser: integrated search, analysis, and visualization of chromatin data
database
summary
CistromeDB
Liu, Xiaole; Mei, Shenglin; Qin, Qian; Wu, Qiu; Sun, Hanfei; Zheng, Rongbin; Zang, Chongzhi; Zhu, Muyuan; Wu, Jiaxin; Shi, Xiaohui; Len, Taing; Liu, Tao; Brown, Myles; Meyer, Cliff
ChIP-Seq and DNase-Seq data in human and mouse
database
summary
CIViCdb
Krysiak, Kilannin; Danos, Arpad M; Saliba, Jason; McMichael, Joshua F; Coffman, Adam; Kiwala, Susanna; Barnell, Erica; Sheta, Lana; Grisdale, Cameron; Kujan, Lynzey; Pema, Shahil; Lever, Jake; Ridd, Sarah; Spies, Nicholas; Andric, Veronica; Chiorean, Andr
Clinical interpretation of variants in cancer
database
summary
CleanEST
Database server for cleansed EST libraries
database
summary
CleanEx
Expression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons
database
summary
ClinicalOmicsDB
Zhang, Bing; Moon, Chang In; Elizarraras, John; Lei, Jonathan; Jia, Byron
ClinicalOmicsDB â€“ Exploring molecular associations of oncology drug responses in clinical trials
database
summary
ClinMAVE
Zhang Zhang; et al.
ClinMAVE: a comprehensive database of clinical interpretations for Multiplexed Assays of Variant Effect
database
summary
ClinVar
Maglott, Donna; Landrum, Melissa; Church, Deanna; Lee, Jennifer M; Riley, George; Jang, Wonhee; Rubinstein, Wendy
ClinVaR is an archive centralizing the management of human sequence variation with clinical significance.
database
summary
ClinVar
Landrum, Melissa; Lee, Jennifer M; Benson, Mark; Brown, Garth; Chen, Chao -; Chitipiralla, Shanmuga; Gu, Baoshan; Hart, Jennifer; Hoffman, Douglas; Jang, Wonhee; Karapetian, Karen; Katz, Kenneth; Liu, Chunlei; Maddipatla, Zenith; Malheiro, Adriana; McDaniel, Kurt; Ovetsky, Michael; Riley, George; Zhou, Zhigang'; Holmes, J.; Kattman, Brandi; Maglott, Donna
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, publ
database
summary
CLIPZ
Mohsen Khorshid
, Christoph Rodak
and Mihaela Zavolan
Experimentally-determined binding sites of RNA-binding proteins
database
summary
CloneDB
Valerie Schneider
Clones and libraries: sequence data, map positions and distributor information
database
summary
ClusterCAD
Keasling, Jay; Eng, Clara; Backman, Tyler; Bailey, Constance; Magnan, Christophe; Martin, Hector; Katz, Leonard; Baldi, Pierre
No description supplied
database
summary
ClusterCAD
Tao, Xavier; LaFrance, Sarah; Xing, Yifei; Nava, Alberto; Martin, Hector; Keasling, Jay D.; Backman, Tyler W.H.
ClusterCAD 2.0: an updated computational platform for chimeric type I polyk
database
summary
ClusterMine360
Kyle Conway
Microbial PKS/NRPS Biosynthesis
database
summary
CMAUP
Chen, Yu Zong; Hou, Dongyue; Lin, Hanbo; Yuhan, Feng; Zhou, Kaicheng; Li, Xingxiu; Yang, Yuan; Wang, Shuaiqi; Yang, Xue; Wang, Jiayu; Zhao, Hui4; Zhang, Xuyao; Fan, Jiajun; Lu, SongLin; Wang, Dan; Zhu, Lyuhan; Ju, Dianwen; Zeng, Xian
CMAUP database update 2023: extended functional and association information of useful plants for biomedical research
database
summary
CMDB
Jin, Xin; Li, Zhichao; Jiang, Xiaosen; Fang, Mingyan; Huang, Shujia; Bai, Yong; Liu, Siyang
Whole-genome sequencing data of 141,000 Chinese individuals
database
summary
CMGSDB
Computational models for gene silencing in C. elegans
database
summary
CMNPD
Liu, Zhenming; Lyu, Chuanyu; Chen, Tong; Qiang, Bo; Liu, Ningfeng; Wang, Heyu; Zhang, Liang-ren
Comprehensive Marine Natural Product Database
database
summary
CMPD
Tang, Petrus; Huang, Po-Jung; Lee, Chi -Ching; Tan, Bertrand; Yeh, Yuan-Ming; Chu, Julie; Chen, Ting-Wen; Lee, Cheng-Yang; Gan, Ruei-Chi; Liu, Hsuan
Cancer Mutant Proteome Database
database
summary
CNAScope
Lingxi Chen; et al.
CNAScope: Pan-Cancer Copy Number Aberration Database with Functional Annotations and Clinical Insights
database
summary
CNCDatabase
Khurana, Ekta; Liu, Eric Minwei; Martinez-Fundichely, Alexander; Bollapragada, Rajesh; Spiewack, Maurice
Cancer drivers at non-coding regions
database
summary
cncRNAdb
Wang, Dong; Huang, Yan; Wang, Jing; Zhao, Yue; Wang, Huafeng; Liu, Tianyuan; Li, Yuhe; Cui, Tianyu; Li, Weiyi; Feng, Yige; Luo, Jiaxin; Gong, Jiaqi; Ning, Lin; Zhang, Yong; Zhang, Yang
Coding and non-coding RNA
database
summary
CODEX
GÃƒÂ¶ttgens, Berthold; SÃƒÂ¡nchez Castillo, Manuel; Ruau, David; Wilkinson, Adam; Ng, Felicia; Hannah, Rebecca; Diamanti, Evangelia; Lombard, Patrick; Wilson, Nicola
ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells
database
summary
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates
Meyer, Xavier;Dib, Linda;Salamin, Nicolas
No description supplied
database
summary
Coexpedia
Lee, Insuk; Yang, Sunmo; Kim, Chanyoung; Hwang, Sohyun; Kim, Eiru; Kim, Hyojin; Shim, Hongsuk
Gene co-expression data mapped to medical subject headings (MeSH).
database
summary
Coffee Genome Hub
dereeper, alexis; Sidibe-Bocs, Stephanie; Rouard, Mathieu; Guignon, Valentin; Ravel, SÃƒÂ©bastien; Tranchant-Dubreuil, Christine; Poncet, ValÃƒÂ©rie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaetan
Coffee community genomics, genetics and breeding data and analysis tools
database
summary
COG
Galperin, Michael Y.; Wolf, Yuri; Makarova, Kira; Vera Alvarez, Roberto; Landsman, David; Koonin, Eugene
No description supplied
database
summary
COGEME Phytopathogenic Fungi and Oomycete EST Database
Soanes, D.M., Talbot, N.J.
Phytopathogenic fungi and oomycete EST database
database
summary
CoGenT++
Complete Genome Tracking database
database
summary
CohesinDB
Nakato, Ryuichiro; Wang, Jiankang
Multi-omics data on cohesin functions
database
summary
coliBASE
A database for
E. coli
Salmonella
and
Shigella
database
summary
Colibri
E. coli
genome database at Institut Pasteur
database
summary
CollecTF
Erill, Ivan; Kilic, Sefa; White, Elliot; Sagitova, Dinara
Experimentally-verified bacterial transcription factor binding sites
database
summary
COLOCdb
Jia, Peilin; Pan, Siyu; Hongen, Kang; Liu, Xinxuan; Li, Shuhua; Yang, Peng; Wu, Mingqiu; Yuan, Na; Lin, Shiqi; Zheng, Qiwen
COLOCdb: a comprehensive resource for multi-model colocalization of complex traits
database
summary
COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia
Pieter Meysman
1,2
, Paolo Sonego
, Luca Bianco
, Qiang Fu
, Daniela Ledezma-Tejeida
, Socorro Gama-Castro
, Veerle Liebens
, Jan Michiels
, Kris Laukens
1,2
, Kathleen Marchal
4,6,7
, Julio Collado-Vides
and Kristof Engelen
3,4
COLections Of Micrcroarrays for Bacterial OrganismS
database
summary
Colorectal Cancer Atlas
Mathivanan, Suresh; Chisanga, David; Keerthikumar, Shivakumar; Pathan, Mohashin; Ariyaratne, Dinuka; Kalra, Hina; Boukouris, Stephanie; Mathew, Nidhi; Ang, Ching-Seng; Sieber, Oliver; Mariadason, John; Dasgupta, Ramanuj,; Chilamkurti, Naveen
Genomic and proteomic annotations from colorectal cancer cell lines
database
summary
COLT-Cancer
Jason Moffat
Essential gene profiles in human cancer cell lines
database
summary
COMBATdb
Knight, Julian; Wang, Dapeng; Kumar, Vinod; Burnham, Katie; Mentzer, Alexander; Marsden, Brian D.
COVID-19 Multi-omics Blood Atlas
database
summary
COMBREX
Computational Bridge to Experiments
database
summary
COMe - Co-Ordination of Metals etc.
Degtyarenko, K., Contrino, S.
Classification of bioinorganic proteins (metalloproteins and some other complex proteins)
database
summary
Comparasite
Watanabe J.
, Wakaguri H.
, Sasaki M.
, Suzuki Y.
and Sugano S.
A database for comparative study of parasite cDNAs
database
summary
Comparative Genometrics
Roten C.-A.H.
, Gamba P.
, Barblan J.-L.
and Karamata D.
DNA walks, nucleotide skews and other biometric measures of prokaryotic genomes
database
summary
Complex Portal
Sucharitha Balu
, Susie Huget
, Juan Jose Medina Reyes
, Eliot Ragueneau
, Kalpana Panneerselvam
, Samantha N. Fischer
, Erin R. Claussen
, Savvas Kourtis
, Colin W. Combe
, Birgit H M Meldal
, Livia Perfetto
Juri Rappsilber
2,7
, Georg Kustatscher
, Kevin Drew
, Sandra Orchard
and Henning Hermjakob
Macromolecular complexes from key model organisms
database
summary
CompoDynamics
Zhang, Zhang; Jiang, Shuai; Du, Qiang; Feng, Changrui; Ma, Lina
Sequence composition and characteristics across genomes
database
summary
ComPPI
Csermely, Peter; Veres, Daniel; Gyurko, David; Thaler, Benedek; Szalay, Kristof; Fazekas, David; Korcsmaros, Tamas
Protein-protein interactions linked to subcellular localization in human, worm, yeast, and fly
database
summary
ComSin
Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, and Oxana V. Galzitskaya
Protein structures in bound and unbound states
database
summary
ConjuPepDB
MÃƒÂ¡ndity, IstvÃƒÂ¡n M; Balogh, Balazs; Ivanczi, Marton; Nizami, Bilal; Beke-Somfai, TamÃƒÂ¡s
Drug-peptide conjugates
database
summary
ConoServer
David Craik
Sequence and structures of peptides expressed by marine cone snails
database
summary
ConsensusPathDB
Herwig, Ralf; Kamburov, Atanas
ConsensusPathDB 2022 - molecular interactions update as a resource for netw
database
summary
ConsensusPathDB
Kamburov, Atanas; Stelzl, Ulrich; Lehrach, Hans; Herwig, Ralf
Database for integration of human functional interactions
database
summary
ConSurf-DB
Sequence conservation profiles of the proteins of known structures
database
summary
ConVarT
Kaplan, Oktay; Pir, Mustafa; Bilgin, Halil; Sayici, Ahmet; Coskun, Fatih; Torun, Furkan; Zhao, Pei; Kang, Yahong; Cevik, Sebiha
Orthologous variants between human, mouse and worm
database
summary
CoPS
Comprehensive peptide signature database
database
summary
CORG - A database for COmparative Regulatory Genomics
Dieterich, C., Wang, H., Rateitschak, K., Luz, H., Vingron, M.
Conserved non-coding sequence blocks
database
summary
CORUM
Ruepp, Andreas; Tsitsiridis, George; Steinkamp, Ralph; Giurgiu, Madalina; Brauner, Barbara; Fobo, Gisela; Frishman, Goar; Montrone, Corinna
CORUM: the comprehensive resource of mammalian protein complexesâ€“â€“2022
database
summary
CORUM
Experimentally verified mammalian protein complexes
database
summary
CoryneRegNet
Baumbach, Jan; Pauling, Josch; RÃƒÆ’Ã‚Â¶ttger, Richard; Tauch, Andreas; Azevedo, Vasco
Corynebacterial transcription factors and regulatory networks
database
summary
COSMIC
Sondka, Zbyslaw; Bindal Dhir, Nidhi; Carvalho-Silva, Denise; Jupe, Steven; Madhumita, Madhumita; McLaren, Karen; Starkey, Mike; Ward, Sari; Wilding, Jennifer; Ahmed, Madiha; Argasinska, Joanna; Beare, David; Singh Chawla, Manpreet; Duke, Stephen; Fasanella, Ilaria; Neogi, Avirup Guha; Haller, Susan; Hetenyi, Balazs; Hodges, Leonie; Holmes, Alex; Lyne, Rachel; Maurel, Thomas; Nair, Sumodh; Pedro, Helder; Sangrador-Vegas, Amaia; Schuilenburg, Helen; Sheard, Zoe; Yong, Siew Yit; Teague, Jon
Catalogue of Somatic Mutations in Cancer
database
summary
CottonGen
Main, Dorrie; Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen; Zheng, Ping; Lee, Taein; Jones, Don; Percy, Richard
Cotton genomics, genetics and breeding
database
summary
CottonMD
Yang, Qing-Yong; Yang, Zhiquan; Wang, Jing; Huang, Yiming; Wang, Shengbo; LuLu, Wei; DongXu, Liu; Weng, Yonglin; Xiang, Jinhai; Zhu, Qiang; Yang, Zhaoen; Nie, Xinhui; Yu, Yu; Yang, Zuoren
Multi-omics data on cotton
database
summary
COV2Var
Zhou, Xiaobo1; Feng, Yuzhou; Yi, Jiahao; Yang, Lin; Wen, Jianguo; Zhao, Weiling; Kim, Pora
COV2Var, a function annotation database of SARS-CoV-2 genetic variation
database
summary
CoV3D
Pierce, Brian; Gowthaman, Ragul; Guest, Johnathan; Yin, Rui; Adolf-Bryfogle, Jared; Schief, William
Experimental coronavirus protein structures
database
summary
CoVDB
Coronavirus genes and genomes
database
summary
COVID19 Drug Repository
Frenkel-Morgenstern, Milana; Tworowski, Dmitry; Gorohovski, Alessandro; Mukherjee, Sumit; Carmi, Gon; Levy, Eliad; Detroja, Rajesh; Biswas Mukherjee, Sunanda
Curated papers on COVID-19 drugs and drug repurposing
database
summary
COVID19db
Zhang, Wenliang; Zhang, Yan; Min, Zhuochao; Mo, Jing; Ju, Zhen; Guan, Wen; Zeng, Binghui,; Liu, Yang; Chen, Jianliang; Zhang, Qianshen; Li, Hanguang; Zeng, Chunxia; Wei, Yanjie; Chan, Godfrey Chi Fung
SARS-CoV-2 transcriptomics and drug discovery
database
summary
CovInDB
Hou, Tingjun; Du, Hongyan; Gao, Junbo; Weng, Gaoqi; Chai, Xin; Pang, Jinping; Kang, Yu; Li, Dan.`; Cao, Dong-Sheng
Covalent Inhibitor DataBase
database
summary
CovInter
Han, Lianyi; AMAHONG, KUERBANNISHA; Zhang, Wei; ZHOU, Ying; Zhang, Song; Yin, Jiayi; Li, Fengcheng; Xu, Hongquan; Yan, Tianci; Yue, Zixuan; Liu, Yuhong; Hou, Tingjun; Qiu, Yunqing; Tao, Lin; Zhu, Feng
Interactions between coronavirus RNAs and host proteins
database
summary
CovPDB
GÃ¼nther, Stefan; Gao, Mingjie; Moumbock, AurÃ©lien A. F.; Qaseem, Ammar; Xu, Qianqing
Covalent inhibitors and their complexes
database
summary
COXPRESdb
Obayashi, Takeshi; Kodate, Shun; Hibara, Himiko; Kagaya, Yuki; Kinoshita, Kengo
COXPRESdb v8: an animal gene coexpression database navigating from a global
database
summary
COXPRESdb
Okamura, Yasunobu; Aoki, Yuichi; Obayashi, Takeshi; Tadaka, Shu; Ito, Satoshi; Narise, Takafumi; Kinoshita, Kengo
Coexpressed genes and networks in human and mouse
database
summary
COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference
Obayashi, Takeshi;Kagaya, Yuki;Aoki, Yuichi;Tadaka, Shu;Kinoshita, Kengo
No description supplied
database
summary
CPDB
The circular permutation database
database
summary
CPLM
Xue, Yu; Zhang, Weizhi; Tan, Xiaodan; Lin, Shaofeng; Gou, Yujie; Han, Cheng; Zhang, Chi; Ning, Wanshan; Wang, Chenwei
Compendium of Protein Lysine Modifications
database
summary
CPLM
Xue, Yu; Liu, Zexian; Wang, Yongbo; Gao, Tianshun; Pan, Zhicheng; Cheng, Han; Yang, Qing; Cheng, Zhongyi; Guo, Anyuan; Ren, Jian
Integrated database of protein lysine acetylation
database
summary
cpnDB
Hill, J.E.
, Penny, S.L.
, Goh, S.H.
and Hemmingsen, S.M.
Chaperonin database
database
summary
CPPsite
Agrawal, Piyush; Bhalla, Sherry; Usmani, Salman; Singh, Sandeep; Chaudhary, Kumardeep; Raghava, Gajendra; Gautam, Ankur
Experimentally validated Cell Penetrating Peptides
database
summary
CR Cistrome
Zhang, Yong; Wang, Qixuan; Huang, Jinyan; Sun, Hanfei; Liu, Jing; Wang, Juan; Wang, Qian; Qin, Qian; Mei, Shenglin; Zhao, Chengchen; Liu, Xiaole
Chromatin Regulators and histone modifications in human and mouse
database
summary
CR-EST - Crop ESTs
C. KÃƒÅ“nne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz
Barley, wheat, pea, and potato ESTs
database
summary
CR2Cancer
Zhang, Jiangwen; Ru, Beibei; Sun, Jianlong; Tong, Yin; Wong, Ching Ngar; Chandra, Aditi; Tang, Acacia Tsz So; Chow, Larry Ka Yue; Wun, Wai Lam; Levitskaya, Zarina
No description supplied
database
summary
CRAMdb
Hu, Shengwei; Lei, Bingbing; Xu, Yueren; Lei, Yunjiao; Li, Cunyuan; Zhou, Ping1; Wang, Limin; Yang, Qing; Li, Xiaoyue; Li, Fulin; Liu, Chuyang; Cui, Chaowen; Chen, Tong; ni, wei
Microbiome metagenomes across animals
database
summary
CRdb
Li, Chunquan; Zhang, Yimeng; Zhang, Yuexin; Song, Chao; Zhao, Xilong; Ai, Bo; Wang, Yuezhu; Zhou, Liwei; Zhu, Jiang6; Feng, Chenchen; Xu, Liyan,; Wang, Qiuyu; Sun, Hong; Fang, Qiaoli; Xu, Xiaozheng; Li, En-Min
Human chromatin regulators
database
summary
Cre Transgenic Database
Nagy, A.
Cre transgenic mouse lines
database
summary
CREAMMIST
Suphavilai, Chayaporn; Yingtaweesittikul, Hatairat; Wu, Jiaxi; Mongia, Aanchal; Peres, Rafael; Ko, Karrie; Nagarajan, Niranjan
Cancer drug dose-reponse across cell lines
database
summary
CREMOFAC
Agrawal S.
1,3
, Chetan Kumar C.
and M.R.S. Rao
1,2
Chromatin remodeling factors
database
summary
CRESTA
Zhixiang Zuo; et al.
CRESTA: A Comprehensive Transcriptome Atlas for Cellular Response to Environmental Stimuli
database
summary
CRISP-view
High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference
database
summary
CRISPR-view
Li, Wei; Cui, Yingbo; Cheng, Xiaolong; Chen, Qing; Song, Bicna; Chiu, Anthony; Gao, Yuan; Dawson, Tyson; Chao, Lumen; Zhang, Wubing; Li, Dian; Zeng, Zexian; Yu, Jijun; Li, Zexu; Teng, Fei; Peng, Shaoliang
Functional genetic screens
database
summary
CRISPRbase
Fan, Jibiao; Shi, Leisheng; Liu, Qi .; Zhu, Zhipeng; Wang, Fan; Song, Runxian; Su, Jimeng; Chen, Xiao,.; Li, Kailong; Xue, Lixiang; Sun, Lichao; Mao, Fengbiao,
CRISPR Base Editing
database
summary
CRISPRepi
Fengbiao Mao
CRISPR-mediated epigenome editing
database
summary
CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs
Chen, Wen;Zhang, Guoqiang;Li, Jing;Zhang, Xuan;Huang, Shulan;Xiang, Shuanglin;Hu, Xiang;Liu, Changning
No description supplied
database
summary
CRISPRoffT
Xiaobo Zhou
CRISPR/Cas off-target data
database
summary
crisprSQL
StÃƒÂ¶rtz, Florian; Minary, Peter,
CRISPR/Cas9 Off-Target Cleavage Assays
database
summary
CRISPRz
Burgess, Shawn; Varshney, Gaurav; Zhang, Suiyuan; Pei, Wuhong; Adomako-Ankomah, Ashrifia; Fohtung, Jacob; Schaffer, Katherine; Carrington, Blake; Maskeri, Anoo; Slevin, Claire; Wolfsberg, Tyra; Sood, Raman
CRISPR single guide RNAs to zebrafish genes
database
summary
CropGS-Hub
Tan, Cong; Chen, Jiaxin; Zhu, Min; Zhang, Chenyang; Wang, Zhihan; Ni, Xuemei; Liu, Yanlin; Wei, Tong; Wei, Xiaofeng; Fang, Xiaodong; Huang, Xuehui; Qiu, Jie; Liu, Huan
CropGS-Hub: A Comprehensive Database of Genotype and Phenotype Resources for Genomic Prediction in Major Crops
database
summary
CROST
Guoliang, Wang; Wu, Song; xiong, zhuang; Qu, Hongzhu; Fang, Xiangdong; Bao, Yi-Ming
CROST: a comprehensive repository of spatial transcriptomics
database
summary
CryptoDB -
Cryptosporidium
database
Cryptosporidium parvum
genome database
database
summary
Crystallography Open Database
Saulius Grazulis
Crystal structures of small molecules
database
summary
CSA - Catalytic Site Atlas
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
Enzyme active sites and catalytic residues in enzymes of known 3D structure
database
summary
CSCD
He, Chunjiang; Feng, Jing1; Chen, Wenbo; Dong, Xin1; Wang, Jun; Mei, Xiangfei; Deng, Jin; Yang, Siqi; Ma, Ronghui; Zhuo, Chenjian; zhang, rongyu; Huang, Xiaoyu; Shao, Lin; Guo, Jing; Liu, Juan; Li, Feng; Wu, Ying; Han, Leng
CSCD2: An integrated interactional database of cancer-specific circular RNA
database
summary
CSCD
Han, Leng; Xia, Siyu; Feng, Jing; Chen, Ke; Ma, Yanbing; Gong, Jing'; Cai, Fangfang; Gao, Yang; Jin, Yuxuan; Chang, Hong; Wei, Lei; He, Chunjiang ,
Circular RNA (circRNA) is a large group of RNA family extensively existed i
database
summary
CSD - Cambridge Structural Database
Crystal structure information for organic and metal organic compounds.
database
summary
CSDBase - Cold Shock Domain database
Weber, M.H.W., Doll, N., Marahiel, M.A.
Cold shock domain-containing proteins
database
summary
CSEA-DB
Zhao, Zhongming; Dai, Yulin; Hu, Ruifeng; Manuel, Astrid; Liu, Andi; Jia, Peilin
Cell type specificity of genetic traits
database
summary
CSS - Carbohydrate Structure Suite
Carbohydrate 3D structures derived from the PDB
database
summary
CSVS
Dopazo, Joaquin; Pena-Chilet, Maria; Roldan, Gema; Perez-Florido, Javier; Ortuno, Francisco Manuel; Carmona, Rosario; Aquino, Virginia; Lopez-Lopez, Daniel; Loucera, Carlos; Fernandez-Rueda, Jose; Gallego, AsunciÃƒÂ³n; Garcia-Garcia, Francisco; Gonzalez-Neir
Spanish genomes and exomes
database
summary
CSVS - The Collaborative Spanish Variability Server
MarÃƒÂa PeÃƒÂ±a-Chilet
1,2,3
, Gema RoldÃƒÂ¡n
, Javier Perez-Florido
1,3,4
, Francisco M. OrtuÃƒÂ±o
1,3,4
, Rosario Carmona
, Virginia Aquino
, Daniel Lopez-Lopez
1,3
, Carlos Loucera
1,3
, Jose L.
Fernandez-Rueda
, AsunciÃƒÂ³n Gallego
, Francisco GarcÃƒÂa-Garcia
, Anna GonzÃƒÂ¡lez-Neira
, Guillermo Pita
, RocÃƒÂo NÃƒÂºÃƒÂ±ez-Torres
, Javier Santoyo-LÃƒÂ³pez
, Carmen Ayuso
,Pablo Minguez
9,10
, Almudena Avila-Fernandez
, Marta Corton
, Miguel Ãƒ\x81ngel Moreno-
Pelayo
11
, MatÃƒÂas Morin
11
, Alvaro Gallego-Martinez
12,13
Jose A. Lopez-Escamez
12,13
, Salud Borrego
14,15
, Guillermo AntiÃƒÂ±olo
14,15
, Jorge Amigo
16
, Josefa Salgado-Garrido
17
,Sara Pasalodos-Sanchez
17
, Beatriz Morte
18
, The Spanish Exome Crowdsourcing
Consortium, Ãƒ\x81ngel Carracedo
16,19
, Ãƒ\x81ngel Alonso
17
, JoaquÃƒÂn Dopazo
1,2,3,4
The knowledge of the genetic variability of the local population is of utmo
database
summary
CTCF Binding Site Database
Experimentally identified and predicted CTCF binding sties
database
summary
CTD
Davis, Allan; Wiegers, Thomas; Johnson, Robin; Sciaky, Daniela; Wiegers, Jolene; Mattingly, Carolyn
Comparative Toxicogenomics Database (CTD): update 2023
database
summary
CTD - Comparative Toxicogenomics Database
Davis, Allan Peter; Johnson, Robin; Murphy, Cynthia; Sciaky, Daniela; Wiegers, Jolene; Wiegers, Thomas; Mattingly, Carolyn
A knowledgebase for curated chemical-gene-disease networks
database
summary
CTDatabase
Cancer-Testis Antigens database
database
summary
CTGA
Tadmouri G.O.
A database for genetic disorders in Arabs
database
summary
CTR-DB v2.0
Jianzhou Jiang, Yajie Ma, Lele Yang, Shurui Ma, Zixuan Yu, Xinyi Ren, Xiangya Kong, Xinlei Zhang, Dong Li, Zhongyang Liu
cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers
database
summary
Cube-DB
Ivana Mihalek
Functional divergence in human protein families
database
summary
CuGenDB
Fei, Zhangjun; Yu, Jingyin; Wu, Shan; Sun, Honghe; Wang, Xin; Tang, Xuemei; Guo, Shaogui; Zhang, Zhonghua; Huang, Sanwen; Xu, Yong "; Weng, Yiqun; Mazourek, Michael; McGregor, Cecilia; Renner, Susanne; Branham, Sandra; Kousik, Chandrasekar; Wechter, Patri
CuGenDBv2: An updated database for cucurbit genomics
database
summary
CutDB
Igarashi Y., Eroshkin A., Gramatikova S., Gramatikoff K., Ying Z., Smith J.W., Osterman, A.L. and Godzik, A.
Community annotation resource for proteases, their substrates and cleavage sites
database
summary
CuticleDB
Structural proteins of Arthropod cuticle
database
summary
CVD Atlas
Jingfa Xiao
Cardiovascular diseases
database
summary
Cyanolyase
Frederic Partensky
Sequences and motifs of the phycobilin lyase protein family
database
summary
CyanoOmicsDB
Tan, Xiaoming; Zhou, Peng; Wang, Li; Liu, Hai; Li, Chunyan; Li, Zhimin; Wang, Jinxiang
Cyanobacteria genomics and transcriptomics
database
summary
Cyanorak
Garczarek, Laurence; Guyet, Ulysse; DorÃƒÂ©, Hugo; Farrant, Gregory; Hoebeke, Mark; GuÃƒÂ©guen-Brillet, Loraine; Bisch, Antoine; Ferrieux, Mathilde; Siltanen, Jukka; Corre, Erwan; Le CorguillÃƒÂ©, Gildas; Ratin, Morgane; Pitt, Franes; Ostrowski, Martin; Conan, Mae
Comparative genomics of cyanobacteria
database
summary
Cybase
Mulvenna J.P., Wang C.K.L. and Craik D.J.
Proteins with cyclic backbones
database
summary
CycleBase
Santos, Alberto; Wernersson, Rasmus; Jensen, Lars
Gene expression profiles from cell-cycle microarray studies
database
summary
Cyclonet
Kolpakov F.
1,2
, Poroikov V.
, Sharipov R.
1,2,4
, Kondrakhin Y
1,2
, Zakharov A.
, Lagunin A.
, Milanesi L.
, and Kel A.
A database on cell cycle regulation
database
summary
CyMoBase
Odronitz F. and Kollmar M.
Database for cytoskeletal and motor proteins
database
summary
Cypriot national mutation database
Disease mutations in the Cypriot population
database
summary
D2P2
Julian Gough
Database of Disordered Protein Predictions
database
summary
Dali database
L. Holm
Fold classification based on structure-structure alignment of proteins
database
summary
DAnCER
Andrei L. Turinsky
, Brian Turner
, Rosanne C. Borja
, James A. Gleeson
, Michael Heath
, Shuye Pu
, Thomas Switzer
, Dong Dong
2,3
, Yunchen Gong
2,3
, Tuan On
1,4
, Xuejian Xiong
, Andrew Emili
2,3,4
, Jack Greenblatt
2,3,4
, John Parkinson
1,4,5,
, Zhaolei Zhang
2,3,4
and Shoshana J. Wodak
1,4,5
Disease-Annotated Chromatin Epigenetics Resource
database
summary
DARC
Roland Beckman
Database for Aligned Ribosomal Complexes
database
summary
DARNED
Pavel Baranov
Database of RNA Editing
database
summary
DART - Drug Adverse Reaction Targets
Drug adverse reaction target database
database
summary
DASHR
Wang, Li-San; Leung, Yuk Yee; Kuksa, Pavel; Amlie-Wolff, Alexandre; Valladares, Otto; Ungar, Lyle; Kannan, Sampath; Gregory, Brian
Database of human small non-coding RNA
database
summary
Database for Bacterial Group II Introns
Candales, Manuel; Duong, Adrian; Hood, Keyar; Li, Teng; Neufeld, Ryan; Sun, Runda; McNeil, Bonnie; Wu, Li; Jarding, Ashley; Zimmerly, Stev
Database for mobile group II introns
database
summary
Database of Genomic Variants (DGV)
MacDonald, Jeffrey; Ziman, Robert; Yuen, Ryan; Feuk, Lars; Scherer, Stephen
Curated catalogue of human genomic structural variation
database
summary
Database of Genomic Variants archive (DGVa)
Lappalainen I, Skipper L, Maguire M, Spalding D, Flicek P
The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants.
database
summary
Database resources of the National Center for Biotechnology Information
Eric W. Sayers
Database resources of the National Center for Biotechnology Information
database
summary
Datanator
Roth, Yosef D; Lian, Zhouyang; Pochiraju, Saahith; Shaikh, Bilal; Karr, Jonathan R
Integrated database of molecular data for integrative biochemical modeling
database
summary
DATF
Anyuan Guo
Database of
Arabidopsis
transcription factors
database
summary
DBAASP
Malak Pirtskhalava, Anthony A Amstrong, Maia Grigolava, Mindia Chubinidze, Evgenia Alimbarashvili, Boris Vishnepolsky, Andrei Gabrielian, Alex Rosenthal, Darrell E Hurt, Michael Tartakovsky
Database of Antimicrobial Activity and Structure of Peptides
database
summary
DBAli
Marti-Renom M.A.
, Pieper U.
, Eswar N.
, Webb B.
, Madhusudhan M.S.
, and Sali A.
Pairwise and multiple structure alignments
database
summary
dbAMP
Lee, Tzong-Yi; Jhong, Chase; Yao, Lantian; Pang, Yuxuan; Li, Zhongyan; Chung, Chia-Ru; Wang, Rulan; Li, Shangfu; Li, Wenshuo; Luo, Mengqi; Ma, Renfei; Huang, Yuqi; Zhu, Xiaoning; Zhang, Jiahong; Feng, Hexiang; Cheng, Qifan; Wang, Chunxuan; Xi, Kun; Wu, Li
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced sca
database
summary
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data
Jhong, Jhih-Hua;Chi, Yu-Hsiang;Li, Wen-Chi;Lin, Tsai-Hsuan;Huang, Kai-Yao;Lee, Tzong-Yi
No description supplied
database
summary
dbAPIS
Yin, Yanbin; Yan, Yuchen; Zheng, Jinfang2; Zhang, Xinpeng
dbAPIS: a database of anti-prokaryotic immune system genes
database
summary
DBASS5/3
Emanuele Buratti
, Martin Chivers
, Gyulin Hwang
and Igor Vorechovsky
Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites
database
summary
dbCAN-HGM
Yanbin Yin; et al.
dbCAN-HGM: CAZyme genes clusters in gut microbiomes of diverse human populations
database
summary
dbCAN-PUL
Yin, Yanbin; Ausland, Catherine; Zheng, Jinfang; Yi, Haidong; Yang, Bowen; Li, Tang; Feng, Xuehuan; Zheng, Bo
Experimentally characterized CAZyme gene clusters
database
summary
dbCAN-seq
Yin, Yanbin; Huang, Le; Zhang, Han; Wu, Peizhi; Entwistle, Sarah; Li, Xueqiong; Yohe, Tanner; Yi, Haidong; Yang, Zhenglu
No description supplied
database
summary
dbCAN_seq
Yin, Yanbin; Zheng, Jinfang1; Hu, Boyang; Zhang, Xinpeng; Ge, Qiwei; Yan, Yuchen; Piyush, Ved; Huang, Le
dbCAN-seq update: CAZyme gene clusters and substates in microbiomes
database
summary
dbCoRC
Huang, Moli; Chen, Ye; Yang, Manqiu; Guo, Anyuan; Xu, Ying; Xu, Liang; Koeffler, H. Phillip
No description supplied
database
summary
dbCRID
Fanlou Kong, Jing Zhu, Jun Wu, Jianjian Peng, Ying Wang, Qing Wang, Songbin Fu, Li-Lian Yuan, and Tongbin Li
Database of Chromosomal Rearrangements In Diseases
database
summary
DBD
Kummerfeld S.K. and Teichmann S.A.
Transcription factor prediction database
database
summary
dbDEMC
Yang, Zhen; Wu, Liangcai; Wang, Anqiang; Tang, Wei; Zhao, Yi; Zhao, Haitao; Teschendorff, Andrew E
Differentially expressed miRNAs in human cancers
database
summary
dbDEPC
Xie, Lu; He, Ying; Zhang, Menghuan; Ju, Yuanhu; Yu, Zhonghao; Lv, Daqing; Sun, Han; Yuan, Weilan; He, Hei; Zhang, Jianshe; Li, Hong ,; Li, Jing ,; Wang-Sattler, Rui; Li, Yixue; Zhang, Guoqing
Differentially Expressed Proteins in Human Cancer
database
summary
dbERGEII
Database of experimental results on gene expression
database
summary
DBETH
Saikat Chakrabarti
Database for Bacterial ExoToxins for Humans
database
summary
dbGaP
Feolo, Michael; Tryka, Kimberly; Hao, Luning; Sturcke, Anne; Jin, Yumi; Wang, Zhen; Ziyabari, Lora; Lee, Moira; Popova, Natalia; Sharopova, Nataliya; Kimura, Masato
Database of Genotypes and Phenotypes
database
summary
dbGuide
Chari, Raj; Gooden, Alexander; Evans, Christine; Sheets, Timothy; Clapp, Michelle
Manually curated and functionally validated guide RNAs
database
summary
dbLEP
Dou L.
, Wang Y.
, Wu S.
, Wang X.
, Mao Y.
, Li L.
, Tang L.
, Wang X.
, Zhao D.
, He F.
and Zhu Y.
Liver proteome expression profiles
database
summary
dbMAE
Savova, Virginia; Patsenker, Jonathan; Vigneau, Sebatien; Gimelbrant, Alexander
Database of monoallelic expression
database
summary
dbMHC
Helmberg W., Feolo M.
Genetic and clinical database of the human MHC
database
summary
dbPSHP
Wang, Junwen J; Li, Mulin; Wang, Lily; Xia, ZhengYuan; Wong, Maria; Sham, Pak
A database of recent positive selection across human populations
database
summary
dbPTM
Lee, Tzong-Yi; Su, Min-Gang; Huang, Kai-Yao; Lu, Cheng-Tsung; Kao, Hui-Ju; Chang, Ya-Han
Post-translational modifications of proteins
database
summary
dbPTM
Lee, Tzong-Yi; Li, Zhongyan; Li, Shangfu; Luo, Mengqi; Jhong, Jhih-Hua; Li, Wenshuo; Yao, Lantian; Pang, Yuxuan; Wang, Zhuo; Wang, Rulan; Ma, Renfei; Huang, Yuqi; Zhu, Xiaoning; Cheng, Qifan; Feng, Hexiang; Zhang, Jiahong; Wang, Chunxuan; Hsu, Justin Bo-K
dbPTM in 2022: an updated database for exploring regulatory networks and fu
database
summary
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications
Huang, Kai-Yao;Lee, Tzong-Yi;Kao, Hui-Ju;Ma, Chen-Tse;Lee, Chao-Chun;Lin, Tsai-Hsuan;Chang, Wen-Chi;Huang, Hsien-Da
No description supplied
database
summary
dbRES
Tao He, Pufeng Du and Yanda Li
A database of known RNA editing sites
database
summary
dbRIP
Song L.
, Wang J.
, Liang P.
, Grover D.
, Batzer M.A.
Retrotransposon insertion polymorphisms in human
database
summary
dbSAP
Shi, Tieliu; Cao, Ruifang; Shi, Yan; Chen, Shuangguan; Ma, Yimin; Chen, Jiajun; Yang, Juan; Chen, Geng
Single Amino acid polymorphisms: SNP-derived variation in human proteins
database
summary
dbSNO
Chen, Yi-Ju; Lu, Cheng-Tsung; Su, Min-Gang; Huang, Kai-Yao; Ching, Wei-Chieh; Yang, Hsiao-Hsiang; Liao, Yen-Chen; Chen, Yu-Ju; Lee, Tzong-Yi
A database of protein S-nitrosylation
database
summary
dbSNP
Lon Phan, Hua Zhang, Qiang Wang, Ricardo Villamarin, Tim Hefferon, Aravinthan Ramanathan, Brandi Kattman
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
database
summary
dbSNP-Q
Scott F. Saccone, Jiaxi Quan, Gaurang Mehta, Raphael Bolze, Prasanth Thomas, Ewa Deelman, Jay A. Tischfield, and John P. Rice
GWAS prioritization tool
database
summary
dbSUPER
Khan, Aziz; Zhang, Xuegong
A database of super-enhancers
database
summary
DBTGR
Sierro N.
, Kusakabe T.
, Park K-J.
, Yamashita R.
, Kinoshita K.
1,3
and Nakai K.
A database of tunicate (
Ciona
) gene regulation
database
summary
DBTMEE
Nakai, Kenta; Park, Sung-Joon; Ohsugi, Miho; Shirahige, K
DataBase of Transcriptome in Mouse Early Embryos
database
summary
DBTSS
Suzuki, Ayako; Wakaguri, Hiroyuki; Yamashita, Riu; Kawano, Shin; Tsuchihara, Katsuya; Sugano, Sumio; Suzuki, Yutaka; Nakai, Kenta
Database of Transcriptional Start Sites
database
summary
DBTSS/DBKERO
Suzuki, Yutaka; Suzuki, Ayako; Kawano, Shin; Mituyama, Toutai; Suyama, Mikita; Kanai, Yae; Shirahige, K; Sasaki, Hiroyuki; Tokunaga, Katsushi; Tsuchihara, Katsuya; Sugano, Sumio; Nakai, Kenta
No description supplied
database
summary
dbVar
Deanna Church
Structural variation in chromosomes: inversions, translocations, insertions and deletions
database
summary
dcGO
Julian Gough
domain-centric Gene Ontology
database
summary
DDA
Wu, Wei; Liang, Yu; Yuan, Qingqing; Zheng, Qijie; Mei, Zilv; Song, Yawei; Yan, Huan; Yang, Jiajie; Wu, Shuheng; Yuan, Jiao
DNA Damage Atlas: an atlas of DNA damage and repair
database
summary
DDBJ
Fukuda, Asami; Kodama, Yuichi; Mashima, Jun; Fujisawa, Takatomo; Ogasawara, Osamu
All known nucleotide and protein sequences
database
summary
DDBJ
Kodama Y; Mashima J; Kodoh K; Ikeo K; Noguchi H; Gojobori T; Fukami-Kobayashi K; Takagi T; Okubo K.
All known nucleotide and protein sequences
database
summary
DDBJ Database updates and computational infrastructure enhancement
Ara, Takeshi; Kodama, Yuichi; Tokimatsu, Toshiaki; Fukuda, Asami; Kosuge, Takehide; Mashima, Jun; Tanizawa, Yasuhiro; Tanjo, Tomoya; Ogasawara, Osamu; Fujisawa, Takatomo; Nakamura, Yasukazu; Arita, Masanori
The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the Nati
database
summary
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data
Kodama, Yuichi;Mashima, Jun;Kosuge, Takehide;Ogasawara, Osamu
No description supplied
database
summary
DDinter
Cao, Dong-Sheng; Xiong, Guoli; Yang, Zhijiang; Yi, Jiacai; Wang, Ningning; Wang, Lei; Zhu, Huimin; Wu, Chengkun; Lu, Aiping; Liu, Shao; Hou, Tingjun
Drug-drug interactions
database
summary
DDMGD
Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir
Associations between genes methylated in diseases
database
summary
Death Domain database
Hyun Ho Park
Protein interaction data for Death Domain superfamily
database
summary
DECIPHER
Swaminathan, Ganesh; Bragin, Eugene; Chatzimichali, Eleni; Wright, Caroline; Hurles, Matthew; Firth, Helen; Bevan, A.
Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
database
summary
Decoys-R-Us
Ram Samudrala and Michael Levitt
Computer-generated protein conformations based on sequence data
database
summary
deepBase
Yang, Jian-Hua; Xie, Fangzhou; Liu, Shurong; Wang, Junhao; Xuan, Jia-Jia; Zhang, Xiaoqin; Qu, Liang-Hu; Zheng, Lingling
No description supplied
database
summary
DeepSpaceDB
Alexis Vandenbon; et al.
DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of cellular spatial organization
database
summary
Defensins Knowledgebase
Seebah S.
, Anita S.
, Zhuo S.W.
, Yong H.C.
, Chua H.
, Chuon D.
, Beuerman R.
, Verma C.S.
Antimicrobial peptides of the defensin family
database
summary
DEG
Zhang, Ren; Luo, Hao.; Lin, Yan; Liu, Tao; Lai, Fei-Liao; Zhang, Chun-Ting; Gao, Feng
No description supplied
database
summary
DEG - Database of Essential Genes
Zhang, Ren; Luo, Hao; Lin, Yan; Gao, Feng ,; Zhang, Chun-Ting
Database of essential genes from bacteria and yeast
database
summary
Degradome Database
Proteases, protease inhibitors and protease mutations in human, chimpanzee, mouse, and rat
database
summary
denovo-db
Turner, Tychele; Yi, Qian; Krumm, Niklas; Huddleston, John; Hoekzema, Kendra; Stessman, Holly; Doebley, Anna-Lisa; Bernier, Raphael; Nickerson, Debbie; Eichler, Evan E.
Human de novo gene variants detected by parent-child sequencing
database
summary
DEPOD
Guangyou Duan, Xun Li, Maja KÃƒÂ¶hn
Human DEPhOsphorylation Database
database
summary
DescribePROT
Sushmita Basu, Bi Zhao, BÃ¡lint BirÃ³, Eshel Faraggi, JÃ¶rg Gsponer, Gang Hu, Andrzej Kloczkowski, Nawar
Malhis, Milot Mirdita, Johannes SÃ¶ding, Martin Steinegger, Duolin Wang, Kui Wang, Dong Xu, Jian Zhang,
Lukasz Kurgan
The DescribePROT database provides convenient access to billions of the ami
database
summary
DESM
Bajic, Vladimir; Salhi, Adil; Essack, Magbubah; Radovanvic, Aleksandar; Marchand, Benoit; Bougouffa, Salim; Antunes, AndrÃƒÂ©; SimÃƒÂµes, Marta; Lafi, Feras; Motwalli, Olaa; Bokhari, Ameerah; Malas, Tareq; Al Amoudi, Soha; Othoum, Ghofran; Alam, Intikhab; Mineta, Katsuhiko; Gao, Xin'; Hoehndorf, Robert; Archer, John A. C.; Gojobori, Takashi
Microbial knowledge exploration systems
database
summary
Dfam
Rob Finn
The Dfam database of repetitive DNA families
database
summary
DG-CST
Disease gene conserved sequence tags
database
summary
DGA
Warren Kibbe
Disease and Gene Annotations database
database
summary
DGIdb
Wagner, Alex; Freshour, Sharon; Kiwala, Susanna; Cotto, Kelsy; Coffman, Adam; McMichael, Joshua; Song, Jonathan; Griffith, Malachi; Griffith, Obi
No description supplied
database
summary
DGIdb
Wagner, Alex H; Cotto, Kelsy; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam; Spies, Gregory; Wollam, Alex; Spies, Nicholas; Griffith, Obi; Griffith, Malachi
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database d
database
summary
DGIdb
Griffith, Obi; Wagner, Alex; Coffman, Adam; Ainscough, Benjamin; Spies, Nicholas; Skidmore, Zachary; Campbell, Katie; Krysiak, Kilannin; Pan, Deng; McMichael, Joshua; Eldred, James; Walker, Jason; Wilson, Richard; Mardis, Elaine; Griffith, Malachi
Drug-gene interaction database
database
summary
DGIdb
Cannon, Matthew; Stevenson, James; Stahl, Kathryn; Basu, Rohit; Coffman, Adam; Kiwala, Susanna; McMichael, Joshua; Kuzma, Kori; Morrissey, Dorian; Cotto, Kelsy; Mardis, Elaine R; Griffith, Obi; Griffith, Malachi; Wagner, Alex
DGIdb 5.0: Rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms
database
summary
DIANA-LncBase
Karagkouni, Dimitra;Paraskevopoulou, Maria D;Tastsoglou, Spyros;Skoufos, Giorgos;Karavangeli, Anna;Pierros, Vasilis;Zacharopoulou, Elissavet;Hatzigeorgiou, Artemis G
DIANA-LncBase v3.0 (www.microrna.gr/LncBase) is a reference repository with
database
summary
DIANA-TarBase
Hatzigeorgiou, Artemis; Karagkouni, Dimitra; Paraskevopoulou, Maria; Chatzopoulos, Serafeim; Vlachos, Ioannis; Tastsoglou, Spyros; Kanellos, Ilias; Papadimitriou, Dimitris; Kavakiotis, Ioannis; Maniou, Sophia; Skoufos, Giorgos; Vergoulis, Thanasis; Dalamagas, Thodoris
DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database d
database
summary
diArk
Kollmar, Martin; Kollmar, Lotte; Hammesfahr, BjÃƒÂ¶rn; Simm, Dominic
A database of eukaryotic sequencing projects
database
summary
Diatom EST Database
ESTs from two diatom algae,
Thalassiosira pseudonana
and
Phaeodactylum tricornutum
database
summary
DictyBase
Genome information, literature and experimental resources for
Dictyostelium discoideum
database
summary
DIDA
Lenaerts, Tom; Gazzo, Andrea; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Van Dooren, Sonia; Smits, Guillaume
DIgenic disease DAtabase
database
summary
DifferentialNET
Yeger-Lotem, Esti; Basha, Omer
No description supplied
database
summary
DIGGER
List, Markus; Louadi, Zakaria; Yuan, Kevin; Gress, Alexander; Tsoy, Olga; Kalinina, Olga; Baumbach, Jan; Kacprowski, Tim
Alternative splicing and protein-protein interactions
database
summary
DIGIT
Anna Tramontano
Database of ImmunoGlobulin sequences and Integrated Tools
database
summary
Digital Ageing Atlas
de MagalhÃƒÂ£es, JoÃƒÂ£o Pedro (contact); Craig, Thomas; Smelick, Chris; Tacutu, Robi; Wuttke, Daniel; Wood, Shona; Stanley, Henry; Janssens, Georges; Savitskaya, Ekaterina; Moskalev, Alexey; Arking, Robert
Human ageing-related data
database
summary
Digital Development Database
Bao, Zhirong; Santella, Anthony; Kovacevic, Ismar; Herndon, Laura; Hall, David; Du, Zhuo
Developmental phenomics, cell-specific gene functions and cell differentiation in C. elegans
database
summary
DIMA
Domain interaction map: experimental and predicted protein domain interactions
database
summary
DIONYSUS
Tatiana Galochkina
Protein-carbohydrate interfaces
database
summary
DiProDB
Database for dinucleotide properties
database
summary
DirectRMDB
Chen, Kunqi; Zhang, Yuxin; Jie, Jiang; Ma, Jiongming; Wei, Zhen; Wang, Yue; Song, Bowen; Meng, Jia; Jia, Gui-Fang; de MagalhÃ£es, JoÃ£o Pedro; Rigden, Daniel J.; huang, daiyun
RNA modifications from direct RNA sequencing
database
summary
DISCO
Chen, Jinmiao; Li, Mengwei; Zhang, Xiaomeng; Siong, Ang Kok; Ling, Jingjing; Raman, Sethi; Lee, Nicole; Ginhoux, Florent
Deep Integration of Single-Cell Omics
database
summary
DisCP-Atlas
Chen Cao; et al.
DisCP-Atlas: a comprehensive resource mapping cellular processes to common and rare human diseases
database
summary
Disease Ontology Knowledgebase
Baron, J. Allen; Johnson, Claudia Sanchez-Beato; Schor, Michael A.; Olley, Dustin;
Nickel, Lance; Felix, Victor; Munro, James B.; Bello, Susan M.; Bearer, Cynthia;
Lichenstein, Richard; Bisordi, Katharine; Koka, Rima; Greene, Carol; Schriml, Lynn M.
DO-KB - Disease Ontology Knowledgebase
database
summary
DiseaseEnhancer
Li, Xia; Zhang, Guanxiong; Shi, Jian; Zhu, Shiwei; Lan, Yujia; Xu, Liwen; Yuan, Huating; Liao, Gaoming; Liu, Xiaoqin; Zhang, Yunpeng; Xiao, Yun
No description supplied
database
summary
DiseaseMeth
Zhang, Yan20; Xing, Jie; Zhai, Ruiyang; Wang, Cong; Liu, Honghao; Zeng, Jiaqi; Zhou, Dianshuang; Zhang, Mengyan; Gu, Yue
DiseaseMeth version 3.0: a major expansion and update of the human disease
database
summary
DiseaseMeth
Yan Zhang
Human disease methylation database
database
summary
DisGeNET
PiÃƒÂ±ero, Janet; Bravo, Ãƒâ‚¬lex; Queralt-Rosinach, NÃƒÂºria; GutiÃƒÂ©rrez-SacristÃƒÂ¡n, Alba; Deu-Pons, Jordi; Centeno, Emilio; GarcÃƒÂa-GarcÃƒÂa, Javier; Sanz, Ferran; Furlong, Laura I.
DisGeNET is a knowledge platform that contains one of the largest available
database
summary
DiSignAtlas
Pan, Jianbo; Zhai, Zhaoyu; Lin, Zhewei; Meng, Xuehang; Zheng, Xiao; Du, Yujia; Li, Zhi; Zhang, Xuelu; Liu, Chang; Zhou, Lu; Zhang, Xu; Tian, Zhihao; Ma, Qinfeng; Li, Jinhao; Li, Qiang
DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics
database
summary
DISNOR
Cesareni, Gianni; Lo Surdo, Prisca; Calderone, Alberto; Iannuccelli, Marta; Licata, Luana; Peluso, Daniele; Castagnoli, Luisa; Perfetto, Livia
No description supplied
database
summary
DisProt
Piovesan, Damiano; Quaglia, Federica; MÃ©szÃ¡ros, BÃ¡lint; Salladini, Edoardo; Hatos, AndrÃ¡s; Pancsa, Rita; Chemes, Lucia B; Pajkos, MÃ¡tyÃ¡s; Lazar, Tamas; PeÃ±a-DÃaz, Samuel; Santos, Jaime; Ã\x81cs, Veronika; Farahi, Nazanin; Ficho, Erzsebet; Aspromonte, Maria Cr
DisProt in 2022: improved quality and accessibility of protein intrinsic di
database
summary
DisProt
Piovesan, Damiano; Aspromonte, Maria Cristina; Nugnes, Maria Victoria; Quaglia, Federica; Bouhraoua, Adel; Tosatto, Silvio
DisProt in 2024: improving function annotation of intrinsically disordered proteins
database
summary
DisProt - Database of Protein Disorder
Information about proteins that lack fixed 3D structure in their native states
database
summary
DisProt: intrinsic protein disorder annotation in 2020
Hatos, AndrÃƒÂ¡s;Hajdu-SoltÃƒÂ©sz, BorbÃƒÂ¡la;Monzon, Alexander M;Palopoli, Nicolas;Ãƒ\x81lvarez, LucÃƒÂa;Aykac-Fas, Burcu;Bassot, Claudio;BenÃƒÂtez, Guillermo I;Bevilacqua, Martina;Chasapi, Anastasia;Chemes, Lucia;Davey, Norman E;DavidoviÃ„â€¡, Radoslav;Dunker, AÃ‚Â Keith;Elofsson, Arne;Gobeill, Julien;Foutel, NicolÃƒÂ¡s SÃ‚Â GonzÃƒÂ¡lez;Sudha, Govindarajan;Guharoy, Mainak;Horvath, Tamas;Iglesias, Valentin;Kajava, Andrey V;Kovacs, Orsolya P;Lamb, John;Lambrughi, Matteo;Lazar, Tamas;Leclercq, Jeremy Y;Leonardi, Emanuela;Macedo-Ribeiro, Sandra;Macossay-Castillo, Mauricio;Maiani, Emiliano;Manso, JosÃƒÂ© A;Marino-Buslje, Cristina;MartÃƒÂnez-PÃƒÂ©rez, Elizabeth;MÃƒÂ©szÃƒÂ¡ros, BÃƒÂ¡lint;MiÃ„\x8DetiÃ„â€¡, Ivan;Minervini, Giovanni;Murvai, Nikoletta;Necci, Marco;Ouzounis, Christos A;Pajkos, MÃƒÂ¡tyÃƒÂ¡s;Paladin, Lisanna;Pancsa, Rita;Papaleo, Elena;Parisi, Gustavo;Pasche, Emilie;BarbosaÃ‚Â Pereira, Pedro J;Promponas, Vasilis J;Pujols, Jordi;Quaglia, Federica;Ruch, Patrick;Salvatore, Marco;Schad, Eva;Szabo, Beata;SzaniszlÃƒÂ³, TamÃƒÂ¡s;Tamana, Stella;Tantos, Agnes;Veljkovic, Nevena;Ventura, Salvador;Vranken, Wim;DosztÃƒÂ¡nyi, Zsuzsanna;Tompa, Peter;Tosatto, Silvio C E;Piovesan, Damiano
No description supplied
database
summary
DistiLD
Lars Juhl Jensen
Diseases and Traits In Linkage Disequilibrium blocks
database
summary
DIVAS
Wei-Yi Cheng, JÃƒÂ¶rg Hakenberg, Shuyu Dan Li and Rong Chen
(Disease Variant Store)
database
summary
DKK
Gomez, Shawn; Berginski, Matthew; Moret, Nienke; Liu, Changchang; Goldfarb, Dennis; Sorger, Peter
Dark Kinome Knowledgebase
database
summary
DMDD
Wilson, Robert; McGuire, Christina; Mohun, Timothy, the DMDD project
Deciphering the Mechanisms of Developmental Disorder
database
summary
DMRdb
Jianbo Pan
Mendelian Randomization-based causal relationships
database
summary
DNAmoreDB
Ponce Salvatierra, Almudena; Boccaletto, Pietro; Bujnicki, Janusz M.
DNAzymes i.e. DNA molecules with catalytic activity
database
summary
DNAproDB: an expanded database and web-based tool for structural analysis of DNAÃ¢â‚¬â€œprotein complexes
Sagendorf, Jared M;Markarian, Nicholas;Berman, Helen M;Rohs, Remo
No description supplied
database
summary
DNAreplication.net
Database for the eukaryotic DNA replication community
database
summary
DNASU Plasmid Repository
Catherine Y. Seiler
, Jin Park
, Amit Sharma
, Preston Hunter
, Padmini Surapaneni
, Casey Sedillo
, James Field
, Rhys Algar
, Andrea Price
, Jason Steel
, Andrea Throop
, Michael Fiacco
, and Joshua LaBaer
DNASU Plasmid Repository, Protein Structure Initiative Material Repository (PSI-MR)
database
summary
DNAtraffic
Joanna Krwawicz
DNA dynamics during the cell cycle
database
summary
dNTPpoolDB
TÃ³th, Judit; Szabo, Judit; Ficho, Erzsebet; Molnar, Daniel; Suranyi, Eva; TrombitÃ¡s, TamÃ¡s; Fuzesi, Dora; Loczi, Hanna; Szijjarto, Peter; HirmondÃ³, Rita; Pancsa, Rita
dNTP concentrations in vivo
database
summary
DO-KB
J Allen Baron , Claudia M SÃ¡nchez-Beato Johnson , Michael A Schor , Dustin Olley , Lance Nickel , Victor Felix , Susan M Bello , Carol Greene , Richard Lichenstein , Katharine Bisordi , Rima Koka , Cynthia Bearer , Regina Macatangay , Nischal Ada , Kaitlin Ballenger , Emily Bliss , Lauren Colliver , Grace Dobbins , Harrison Heitzig , Shannan Dixon , Patrick Semesky , Jennifer Garth , Matthew Fairchild , Peter Gaskin , Sarina Zahid , Rachel Castillo , Sarah Edwards , Astrid Widjaja , Yamei Usui , Erin Lynch , Melissa Clarkson , Todd Detwiler , Lynn M Schrim
Ontology for a variety of human diseases
database
summary
DoBISCUIT
Natsuko Ichikawa
Database Of BIoSynthesis clusters CUrated and InTegrated
database
summary
DockCoV2
In silico drug docking against SARS-CoV2 targets
database
summary
Dockground
Protein-protein interfaces in co-crystallized protein structures
database
summary
dog10k
Guo-Dong Wang
Dog omics
database
summary
DoGSD
Wang, Guo-Dong; Bai, Bing; Zhao, Wen-Ming; Tang, Bi-Xia; Wang, Yan-Qing; Wang, Lu; Zhang, Zhang; Yang, He-Chuan; Irwin, David; Zhang, Ya-Ping; Liu, Yan-Hu; Zhu, Jun-Wei
Dog and wolf whole genome variation browser
database
summary
DOMINE
Known and predicted protein domain interactions observed in PDB entries,
database
summary
DOMINO
Domain peptide interactions
database
summary
DomIns - Database of Domain Insertions
Aroul-Selvam R.
and Sasidharan R.
Domain insertions in known protein structures
database
summary
DOMMINO
Dmitry Korkin
Database of MacroMolecular INteractions
database
summary
DOO
Longjun Wu; et al.
DOO: Integrated Multi-Omics Resources for Deep Ocean Organisms
database
summary
DoOP - Databases of Orthologous Promoters
Barta E.
, SebestyÉn E.
, PÁlfy T.B.
, TÓth G.
, Ortutay C.P.
and Patthy L.2
Clusters of orthologous upstream sequences from chordates and plants
database
summary
DoriC
Dong, Mei-Jing; Luo, Hao.; Gao, Feng
DoriC 12.0, an updated database of replication origins in both complete and
database
summary
DoriC
Chun-Ting Zhang
DoriC regions in bacterial and archaeal genomes
database
summary
DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids
Luo, Hao;Gao, Feng
No description supplied
database
summary
doRiNA
Blin, Kai; Dieterich, Christoph; Wurmus, Ricardo; Rajewsky, Nikolaus; Landthaler, Markus; Akalin, Altuna
Database of RNA interactions in post-transcriptional regulation
database
summary
DPRP
Cheng, Chao; Tseng, Yu-Ting; Tzeng, David; Ung, Matthew; Liu, Chun-Chi
A database of phenotype-specific regulatory programs derived from transcription factor binding data
database
summary
DPVweb
Adams M.J. and Antoniw J.F.
Viruses of plants, fungi and protozoa
database
summary
Dr.VIS
Yang, Xiaobo; Li, Ming -; Liu, Qi ,; Zhang, Yabing; Qiang, Junyan; Wan, Xueshuai; Wang, Anqiang; Zhang, Haohai; Zhu, Chengpei; Lu, X in; Mao, Yilei; Sang, Xinting; Zhao, Haitao; Zhao, Yi; zhang, xiaoyan
Chromosomal integration sites of viruses in the human tumor
database
summary
DRAMP
Heng Zheng
Antimicrobial peptides
database
summary
DRASTIC
Database resource for analysis of signal transduction in plant cells
database
summary
DreamBASE
Qu, Liang-Hu; Zheng, Ling-Ling; Zhou, Ke-Ren; Liu, Shun; Zhang, Ding-Yao; Wang, Ze-lin; Chen, Zhi-Rong; Yang, Jian-Hua
DNA regulation, RNA expression and protein translation of pseudogenes in human and mouse.
database
summary
DRESIS
Xhaard; Heiskanen; et al.
DRESIS 2026: the comprehensive landscape of drug resistance information and its molecular mechanisms
database
summary
DRESIS
Zhu, Feng; Sun, Xiuna; Wei, Zhangle; Yu, Xinyuan; Liu, Kaixuan; Yao, Shun; Ni, Zheng; Wang, Hanbing; Zhao, Ziming; Zhang, Yinpeng; Ding, Hanlu; Zhang, Yintao; Liu, Zhiguo; Xiao, Mang
Drug resistance
database
summary
DriverDB
Cheng, Wei-Chung; Liu, Chia-Hsin; Lai, Yo-Liang; Shen, Pei-Chun; Liu, Hsiu-Cheng; Tsai, Meng-Hsin; Yu-De, Wang; Lin, Wen-Jen; Chen, Fang-Hsin; Li, Chia-Yang; Wang, Shu-Chi
DriverDBv4: A Multi-Omics Integration Database for Cancer Driver Gene Research
database
summary
DriverDBv2
I-Fang Chung, Chen-Yang Chen, Shih-Chieh Su, Chia-Yang Li, Kou-Juey Wu, Hsei-Wei Wang and Wei-Chung Cheng
DriverDB, a database that incorporates >9500 cancer-related RNA-seq dataset
database
summary
DrLLPS: a data resource of liquidÃ¢â‚¬â€œliquid phase separation in eukaryotes
Ning, Wanshan;Guo, Yaping;Lin, Shaofeng;Mei, Bin;Wu, Yu;Jiang, Peiran;Tan, Xiaodan;Zhang, Weizhi;Chen, Guowei;Peng, Di;Chu, Liang;Xue, Yu
No description supplied
database
summary
DRMref
Song, Qianqian; Liu, Xiaona; Yi, Jiahao; Li, Tina; Wen, Jianguo; Kim, Pora; Zhou, Xiaobo1
DRMref: comprehensive reference map of drug resistance mechanisms
database
summary
DroID - Drosophila Interactions Database
Yu J, Pacifico S., Guest G., Parrish J.R., and Finley R.L., Jr.
Drosophila gene and protein interaction data
database
summary
Drosophila polymorphism database
Casillas S., Petit N. and Barbadilla A.
Drosophila polymorphism database
database
summary
DroSpeGe
Gilbert D.G.
Drosophila Species Genomes
database
summary
DRTF
Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J.
Database of rice transcription factors
database
summary
Drug2Gene
Helge G Roider
, Nadia Pavlova
, Ivaylo Kirov
, Stoyan Slavov
, Todor Slavov
, Zlatyo Uzunov
and Bertram Weiss
Drug2Gene is a free multi-species drug-target knowledge base
database
summary
DrugBank
Wishart, David; Law, Vivian; Knox, Craig; Djoumbou, Yannick; Guo, An Chi; Jewison, Tim; Liu, Yifeng; Maciejewski, Adam; Arndt, David; Neveu, Vanessa; Tang, Alexandra; Gabriel, Geraldine; Ly, Carol; Adamjee, Sakina; Dame, Zerihune; Han, Beomsoo; Wilson, Michael.; Zhu, You
Combined information on drugs and drug targets
database
summary
DrugBank
Wishart, David; Knox, Craig; Wilson, Michael; Klinger, Christen; Franklin, Mark; Oler, Eponine; Wilson, Alex; Pon, Allison; Cox, Jordan; Chin, Na; Strawbridge, Seth; Garcia-Patino, Marysol; Kruger, Ray; Sivakumaran, Aadhavya; Sanford, Selena; Doshi, Rahil; Khetarpal, Nitya; Fatokun, Omolola; Doucet, DaphnÃ©e; Zubkowski, Ashley; Jackson, Hayley; Harford, Karxena; Anjum, Afia; Zakir, Mahi; Wang, Fei; Tian, Siyang; Lee, Brian; Peters, Harrison; Wang, Ruo; Nguyen, Tue; So, Denise; Sharp, Matthew; da Silva, Rodolfo; Gabriel, Cyrella; Scantlebury, Joshua; Jasinski, Marissa; Ackerman, David; Jewison, Tim; Sajed, Tanvir; Gautam, Vasuk
No description supplied
database
summary
DrugCentral
Oprea, Tudor; Avram, Sorin; Bologa, Cristian; Holmes, Jayme; Bocci, Giovanni; Wilson, Thomas; Nguyen, Dac-Trung; Curpan, Ramona; Halip, Lili; Bora, Alina; Yang, Jeremy; Knockel, Jeffrey; Sirimulla, Suman; Ursu, Oleg
Active ingredients of approved pharmaceutical products, indications. and mode of action
database
summary
DrugCentral
Oprea, Tudor; Avram, Sorin; Wilson, Thomas; Curpan, Ramona; Halip, Lili; Borota, Ana; Bora, Alina; Bologa, Cristian; Holmes, Jayme; Knockel, Jeffrey; Yang, Jeremy
DrugCentral 2023 extends human clinical data and integrates veterinary drug
database
summary
DrugMAP
Chen, Yu Zong; Li, Fengcheng; Yin, Jiayi; Lu, Mingkun; Mou, Minjie; Li, Zhaorong; Tan, Ying; Wang, Shanshan; Chu, Xinyi; Dai, Haibin; Zeng, Su; Zhu, Feng
Molecular Atlas and Pharma-information of drugs
database
summary
DrugSpaceX
Zheng, Mingyue; Yang, Tianbiao; Li, Zhaojun; Chen, Yingjia; Feng, Dan; Wang, Guangchao; Fu, Zunyun; Ding, Xiaoyu; Tan, Xiaoqin; Zhao, Jihui; Luo, Xiaomin; Chen, Kaixian; Jiang, Hualiang
100 million compounds for virtual screening
database
summary
DRYGin
Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, and Charles Boone
Data Repository for Yeast Genetic Interaction Networks
database
summary
DSD
Toseland C.P., McSparron H., Doytchinova I.A., and Flower D.R.
Database of dehydrogenase enzyme stereospecificities
database
summary
DSDBASE
Vinayagam, A., Pugalenthi G., Rajesh R., Sowdhamini, R.
Database on disulfide bonds in proteins
database
summary
DSMM - a Database of Simulated Molecular Motions
Finocchiaro, G.
, Wang, T.
, Hoffmann, R.
, Gonzalez, A.
, Wade, R.C.
Database of Simulated Molecular Motions
database
summary
DualSeqDB
Torrent, Marc; Macho RendÃƒÂ³n, Javier; Lang, Benjamin; Ramos Llorens, Marc; Tartaglia, Gian Gaetano
Dual RNA-seq host-pathogen sequencing
database
summary
DupScan
Lu, Jianguo; Sun, Jialiang; Liu, Jian; Huang, Peilin
Vertebrate genome duplications
database
summary
Dynamic Proteomics
Frenkel-Morgenstern, M.
, Cohen, A.A.
Geva-Zatorsky, N.
Eden, E.
Prilusky, J.
, Issaeva, I.
, Sigal, A.
, Cohen-Saidon, C.
Liron, Y.
Cohen, L.
Danon, T.
Perzov, N.
, and Alon, U.
Dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
database
summary
DynaProt 2D
Drews, O. and Gorg, A.
Proteome database of
Lactococcus lactis
database
summary
EBCD
Philip Gribbon
European Chemical Biology Database
database
summary
EBI Enzyme Portal
Christoph Steinbeck
Various kinds of information about enzymes: small-molecule chemistry, biochemical pathways and drug compounds
database
summary
EBI Genomes
EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
database
summary
EBI Metagenomics
Mitchell, Alex; Scheremetjew, Maxim; Denise, Hubert; Potter, Simon; Tarkowska, Aleksandra; Qureshi, Matloob; Salazar, Gustavo; Pesseat, Sebastien; Boland, Miguel; Hunter, Fiona; Ten Hoopen, Petra; Alako, Blaise; Amid, Clara; Wilkinson, Darren; Curtis, Thomas; Cochrane, Guy; Finn, Robert
EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use
database
summary
EBI Metagenomics
Mitchell, Alex; Bucchini, Francois; Cochrane, Guy; Denise, Hubert; Ten Hoopen, Petra; Fraser, Matthew; Pesseat, Sebastien; Potter, Simon; Scheremetjew, Maxim; Sterk, Peter; Finn, Robert
An automated pipeline for the analysis and archiving of metagenomic data
database
summary
EBI patent sequences
Weizhong Li, Hamish McWilliam, Ana Richart de la Torre, Adam Grodowski, Irina Benediktovich, Mickael Goujon, Stephane Nauche, and Rodrigo Lopez
Non-redundant databases of patent DNA and protein sequences
database
summary
EBI resources
Cantelli, Gaia; Cochrane, Guy; Brooksbank, Catherine; McDonagh, Ellen; Flicek, Paul; McEntyre, Johanna; Birney, Ewan; Apweiler, Rolf
Database resources of the European Bioinformatics Institute
database
summary
eBLOCKS
Su Q., Lu L., Saxonov S. and Brutlag D.L.
Highly conserved protein sequence blocks
database
summary
ECgene
Genome annotation for alternative splicing
database
summary
Echinobase
Hinman, Veronica; Arshinoff, Bradley; Cary, Gregory; Karimi, Kamran; Foley, Saoirse; Agalakov, Sergei; Delgado, Francisco; Lotay, Vaneet; Ku, Carolyn; Pells, Troy; Beatman, Thomas; Kim, Eugene; Cameron, R. Andrew; Vize, Peter; Telmer, Cheryl; Croce, Jenif
Echinoderm genomics
database
summary
EciD
Protein interaction predictions by several different methods
database
summary
ECMDB
David Wishart
Escherichia coli Metabolome Database
database
summary
ECO
Giglio, Michelle; Nadendla, Suvarna; Tauber, Rebecca; Munro, James; Quaglia, Federica; MÃ©szÃ¡ros, BÃ¡lint; Olley, Dustin; Hobbs, Elizabeth; Goralski, Stephen; Chibucos, Marcus; Mungall, Chris; Tosatto, Silvio; Erill, Ivan
Evidence and Conclusion Ontology
database
summary
ECOD
Schaeffer, Randy; Liao, Yuxing; Cheng, Hua; Grishin, Nick
Evolutionary Classification of Protein Domains
database
summary
ECOdrug
Verbruggen, Bas; Gunnarsson, Lina; Kristiansson, Erik,; Ãƒâ€“sterlund, Tobias; Owen, Stewart; Snape, Jason; Tyler, Charles
No description supplied
database
summary
EcoDrug PLUS
Ashenafi Legehar1 , SiobhÃ¡n Monaghan2 , Mael Briand1 , Akseli NiemelÃ¤1 , Leo Ghemtio1 , Ziaurrehman Tanoli3 , A. Ross Brown2 , Charles R. Tyler2 , Henri Xhaard1
EcoDrug PLUS: an advanced database for drug target conservation analysis and environmental risk assessment
database
summary
EcoliWiki
Jim Hu
Community-based pages about non-pathogenic E. coli
database
summary
ECRbase
Loots G.G. and Ovcharenko I.
Evolutionary conserved regions, promoters, and transcription factor binding sites
database
summary
EDAS - EST-Derived Alternative Splicing Database
Nurtdinov, R.N., Neverov, A.D., Mironov, A.A., and Gelfand, M.S.
Alternative splicing deduced from EST data
database
summary
Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human
Niu, Guangyi;Zou, Dong;Li, Mengwei;Zhang, Yuansheng;Sang, Jian;Xia, Lin;Li, Man;Liu, Lin;Cao, Jiabao;Zhang, Yang;Wang, Pei;Hu, Songnian;Hao, Lili;Zhang, Zhang
No description supplied
database
summary
EDomics
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang and Bo Dong
Comparative multi-omics for animal Evo-Devo
database
summary
EDULISS (currently unavailable)
Kun-Yi Hsin
, Hugh P. Morgan
, Steven R. Shave
, Andrew C. Hinton
, Paul Taylor
and Malcolm D. Walkinshaw
EDinburgh University Ligand Selection System
database
summary
EENdb
Bo Zhang
Engineered endonucleases: zinc finger nucleases and transcription activator-like effector nucleases
database
summary
eF-site - Electrostatic surface of Functional site
Electrostatic potentials and hydrophobic properties of the active sites
database
summary
Effective
Marc-Andre Jehl, Roland Arnold, and Thomas Rattei
Predicted secreted bacterial proteins
database
summary
EGA
Rambla, Jordi; Freeberg, Mallory; Fromont, Lauren; D'Altri, Teresa; Foix, Anna; Izquierdo Ciges, Jorge; Jene, Aina; Kerry, Giselle; Moldes, Mauricio; Ariosa, Roberto; Bahena, Silvia; Barrowdale, Daniel; Casado, Marcos; Fernandez-Orth, Dietmar; Garcia-Lina
European Genome-Phenome Archive
database
summary
eggNOG
HernÃ¡ndez-Plaza, Ana; Szklarczyk, Damian; Botas, Jorge; Cantalapiedra, Carlos P.; Giner Lamia, joaquin; Mende, Daniel R; Kirsch, Rebecca; Rattei, Thomas; Letunic, Ivica,; Jensen, Lars,; Bork, Peer; von Mering, Christian; Huerta Cepas, Jaime
eggNOG 6.0: Enabling comparative genomics across 12,535 organisms
database
summary
eggNOG
Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldon, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars,; von Mering, Christian; Bork, Peer
A database of orthology relationships, functional annotation, and gene evolutionary histories.
database
summary
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Huerta-Cepas, Jaime;Szklarczyk, Damian;Heller, Davide;HernÃƒÂ¡ndez-Plaza, Ana;Forslund, Sofia K;Cook, Helen;Mende, Daniel R;Letunic, Ivica;Rattei, Thomas;Jensen, LarsÃ‚Â J;vonÃ‚Â Mering, Christian;Bork, Peer
No description supplied
database
summary
EHFPI
Bo, Xiaochen; Liu, Yang; Xie, Dafei; Bai, Hui; Han, Lu; Li, Fei; Wang, Shengqi
Essential Host Factors for Pathogenic Infection
database
summary
EK3D
Rathinavelan, Thenmalarchelvi; Reddy, Kunduru; Nair, Sanjana
Capsular polysaccharide (K antigen) structures of various serotypes of
E. coli
database
summary
EKPD
Xue, Yu; Wang, Yongbo; Liu, Zexian; Cheng, Han; Pan, Zhicheng; Yang, Qing; Guo, Anyuan
Eukaryotic Kinase and Phosphatase Database
database
summary
ELM
Gouw, Marc; Michael, Sushama; SÃƒÂ¡mano-SÃƒÂ¡nchez, Hugo; Kumar, Manjeet; Zeke, AndrÃƒÂ¡s; Lang, Benjamin; Bely, Benoit; Chemes, Lucia; Davey, Norman; Deng, Ziqi; Diella, Francesca.; Guerth, Clara-Marie; Huber, Ann-Kathrin; Kleinsorg, Stefan; Schlegel, Lara; Palopoli, Nicolas; Van Roey, Kim; RemÃƒÂ©nyi, Attila; Dinkel, Holger; Gibson, Toby
The eukaryotic linear motif resource
database
summary
ELM
Kumar, Manjeet; Michael, Sushama; Alvarado Valverde, Jesus; Zeke, AndrÃ¡s; Lazar, Tamas; Dobson-Kalman, Zsofia; Nagpal, Anurag; Mac Donagh, Juan; Griffin, Juan; Van Roey, Kim; Glavina, Juliana; Palopoli, NicolÃ¡s; Bhardwaj, Rajesh; Pascarelli, Stefano; Dobson, LÃ¡szlÃ³; Nagy-Kanta, Eszter; Diella, Francesca.; Suarez, Carmen Florencia; Dean, Kellie; Davey, Norman; Pancsa, Rita; Chemes, Lucia; Gibson, Toby J
ELM - The Eukaryotic Linear Motif resource - 2024 update
database
summary
ELM
Kumar, Manjeet; Michael, Sushama; Alvarado Valverde, Jesus; MÃ©szÃ¡ros, BÃ¡lint; SÃ¡mano-SÃ¡nchez, Hugo; Zeke, AndrÃ¡s; Dobson, LÃ¡szlÃ³; Lazar, Tamas; Ã–rd, Mihkel; Nagpal, Anurag; Farahi, Nazanin; KÃ¤ser, Melanie; Kraleti, Ramya; Davey, Norman; Pancsa, Rita; Chem
The Eukaryotic Linear Motif resource - 2022 release
database
summary
ELM - Eukaryotic Linear Motif: functional sites in eukaryotic proteins
Dinkel, Holger; Van Roey, Kim; Michael, Sushama; Davey, Norman E; Weatheritt, Robert; Born, Diana; Speck,
Eukaryotic linear motif: functional sites in eukaryotic proteins
database
summary
ELMÃ¢â‚¬â€\x9Dthe eukaryotic linear motif resource in 2020
Kumar, Manjeet;Gouw, Marc;Michael, Sushama;SÃƒÂ¡mano-SÃƒÂ¡nchez, Hugo;Pancsa, Rita;Glavina, Juliana;Diakogianni, Athina;Valverde, JesÃƒÂºs Alvarado;Bukirova, Dayana;Ã„Å’alyÃ…Â¡eva, Jelena;Palopoli, Nicolas;Davey, Norman E;Chemes, LucÃƒÂa B;Gibson, Toby J
No description supplied
database
summary
EMAGE
Richardson L, Venkataraman S, Stevenson P, Yang Y, Moss J, Graham L, Burton N, Hill B, Rao J, Baldock RA, Armit C.
Edinburgh Mouse Atlas gene expression database
database
summary
EmAtlas
Zuo, Yongchun; Zheng, Lei; Liang, Pengfei; Long, Chunshen; Li, Haicheng; Li, Hanshuang; Liang, Yuchao; He, Xiang; Xi, Qilemuge; Xing, Yongqiang
Spatiotemporal multi-omics of mammalian embryogenesis
database
summary
EMDataBank
Catherine L. Lawson
, Matthew L. Baker
, Christoph Best
, Chunxiao Bi
, Matthew Dougherty
, Powei Feng
, Glen van Ginkel
, Batsal Devkota
, Ingvar Lagerstedt
, Steven J. Ludtke
, Richard H. Newman
, Tom J. Oldfield
, Ian Rees
, Gaurav Sahni
, Raul Sala
, Sameer Velankar
, Joe Warren
, John D. Westbrook
, Kim Henrick
, Gerard J. Kleywegt
, Helen M. Berman
and Wah Chiu
3D cryo-electron microscopy maps, models and metadata
database
summary
EMDB
Turner, Jack; Abbott, Sanja; Fonseca, Neli; Carrijo, Lucas; Duraisamy, Amudha Kumari; Salih, Osman; Wang, Zhe; Kleywegt, Gerard; Morris, Kyle; Patwardhan, Ardan; Burley, Stephen; Crichlow, Gregg; Feng, Zukang; Flatt, Justin W.; Ghosh, Sutapa; Hudson, Brian; Lawsone, Catherine; Liang, Yu He; Peisach, Ezra; Persikova, Irina; Sekharan, Monica; Shao, Chenghua; Young, Jasmine Y; Velankar, Sameer; Armstrong, David; Bage, Marcus; Bueno, Weslley; Evans, Genevieve; GÃ¡borovÃ¡, Romana; Ganguly, Sudakshina; Gupta, Deepti; Harrus, Deborah; Tanweer, Ahsan; Kurisu, Genji; Cho, Hasumi; Ikegawa, Yasuyo; Kengaku, Yumiko; Kim, Ju Yaen; Niwa, Satomi; Sato, Junko; Takuwa, Ayako; Yu, Jian; Hoch, Jeffrey; Xu, Wenqing; Zhang, Weizhe; Ma, Xiaodan; Bansal, Manju; Rangannan, Vetriselvi
EMDB - the Electron Microscopy Data Bank
database
summary
EMPIAR
Patwardhan, Ardan; Iudin, Andrii; Korir, Paul; Somasundharam, Sriram; Weyand, Simone; Cattavitello, Cesare; Fonseca, Neli; Salih, Osman; Kleywegt, Gerard
The Electron Microscopy Public Image Archive
database
summary
ENCODE
Cherry, J. Michael; Davis, Carrie; Hitz, Benjamin; Sloan, Cricket; Chan, Esther; Davidson, Jean; Gabdank, Idan; Hilton, Jason; Jain, Kriti; Baymuradov, Ulugbek; Narayanan, Aditi; Onate, Kathrina; Graham, Keenan; Miyasato, Stuart; Dreszer, Timothy; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has deve
database
summary
ENCODE DCC
Cherry, J. Michael; Sloan, Cricket; Chan, Esther; Davidson, Jean; Malladi, Venkat; Strattan, J Seth; Hitz, Benjamin; Gabdank, Idan; Narayanan, Aditi; Ho, Marcus; Lee, Brian; Rowe, Laurence; Dreszer, Timothy; Roe, Greg R; Podduturi, Nikhil Reddy; Tanaka, Forrest; Hong, Eurie
No description supplied
database
summary
ENCODE Project at UCSC
Rosenbloom, Kate
; Dreszer, Timothy
; Malladi, Venkat
; Long, Jeffrey
; Sloan, Cricket
; Raney, Brian
; Cline, Melissa
; Karolchik, Donna
; Barber, Galt
; Clawson, Hiram
; Diekhans, Mark
; Fujita, Pauline
; Goldman, Mary
; Gravell, Robert
; Kuhn, Robert
; Harte, Rachel
; Hinrichs, Angie
; Kirkup, Vanessa
; Learned, Katrina
; Maddren, Morgan
; Meyer, Laurence
; Pohl, Andy
1,2
; Rhead, Brooke
; Wong, Mathew
; Zweig, Ann
; Haussler, David
1,3
; Kent, Jim
Encyclopedia of DNA Elements, all functional elements in the human genome
database
summary
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins
Sarti, Edoardo;Aleksandrova, Antoniya A;Ganta, Srujan K;Yavatkar, Amarendra S;Forrest, Lucy R
No description supplied
database
summary
ENdb: a manually curated database of experimentally supported enhancers for human and mouse
Bai, Xuefeng;Shi, Shanshan;Ai, Bo;Jiang, Yong;Liu, Yuejuan;Han, Xiaole;Xu, Mingcong;Pan, Qi;Wang, Fan;Wang, Qiuyu;Zhang, Jian;Li, Xuecang;Feng, Chenchen;Li, Yanyu;Wang, Yuezhu;Song, Yiwei;Feng, Ke;Li, Chunquan
No description supplied
database
summary
ENdb: An experimentally supported enhancer database for human and mouse
Bai, Xuefeng;Shi, Shanshan;Ai, Bo;Jiang, Yong;Liu, Yuejuan;Han, Xiaole;Xu, Mingcong;Pan, Qi;Wang, Fan;Wang, Qiuyu;Zhang, Jian;Li, Xuecang;Feng, Chenchen;Li, Yanyu;Wang, Yuezhu;Song, Yiwei;Feng, Ke;Li, Chunquan
ENdb is a database documenting 2003 experimentally validated enhancer interactions and 741 diseases/phenotypes through manually curating of over 20,000 published literature.Through reviewing 5,518 published literatures, the current release of ENdb2.0 documents 2,003 experimentally validated enhancers and their related information, including: 776 cell names, 267 tissue names,969 target genes, 556 transcription factors, 741 diseases and 2,003 functions for human and mouse.
database
summary
EndoNet
Potapov A.
, Liebich I.
1,2
, DÃƒÆ’Ã‚Â¶nitz J.
, Schwarzer K.
, Sasse N.
, Schoeps T.
, Crass T.
and Wingender E.
1,2
Information about the components of endocrine networks
database
summary
EndoQuad
Qian, Sheng Hu; Shi, Meng-Wei; Xiong, Yu-Li; Zhang, Yuan; Zhang, Ze-Hao; Song, Xue-Mei; Deng, Xin-Yin; Chen, Zhen-Xia
EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database
database
summary
enhancer3D
Michal Wlasnowolski; et al.
enhancer3D: 3D Chromatin Structures and Enhancer-Promoter Distances in the Human Genome
database
summary
EnhancerAtlas 2.0
Gao, Tianshun;Qian, Jiang
Enhancers are a class of cis-regulatory elements that can increase gene tra
database
summary
ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins
TakÃ‚Â Leung, Ricky Wai;Jiang, Xiaosen;Chu, Ka Hou;Qin, Jing
No description supplied
database
summary
Ensembl
Yates, Andrew; Austine-Orimoloye, Olanrewaju; Azov, Andrey; Barba, Matthieu; Barnes, If; Barrera-Enriquez, Vianey; Becker, Arne; Bennett, Ruth; Berry, Andrew.; Bhai, Jyothish; Kaur Bhurji, Simarpreet; Branco Lins,
Ensembl genome browser
database
summary
Ensembl COVID-19 resource
Yates, Andrew; De Silva, Nishadi; Bhai, Jyothish; Chakiachvili, Marc; Contreras Moreira, Bruno; Cummins, Carla; Frankish, Adam; Gall, Astrid; Genez, Thiago; Howe, Kevin; Hunt, Sarah; Martin, Fergal; Moore, Benjamin; Ogeh, Denye; Parker, Anne; Parton, Andr
Integrated public SARS-CoV-2 data
database
summary
Ensembl Genomes
Kersey, Paul; Allen, James; Allot, Alexis; Barba, Matthieu; Boddu, Sanjay; Bolt, Bruce; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Grabmueller, Christoph; Kumar, Navin; Liu, Zicheng; Maurel, Thomas; Moore, Benjamin; McDowall, Mark; Maheswari, Uma; Naamati, Guy; Newman, Victoria; Ong, ChuangKee; Paulini, Michael; Pedro, Helder; Perry, Emily,; Russell, Matthew; Sparrow, Helen; Tapanari, Electra; Taylor, Kieron; Vullo, Alessandro; Williams, Gareth; Zadissa, Amonida; Olson, Andrew J; Stein, Joshua; Wei, Sharon; Tello-Ruiz, Marcela; Ware, Doreen; Luciani, Aurelien; Potter, Simon; Finn, Robert; Urban, Martin; Hammond-Kosack, Kim; Bolser, Daniel; De Silva, Nishadi; Howe, Kevin; Langridge, Nicholas; Maslen, Gareth; Staines, Daniel; Yates, Andrew
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource
database
summary
ENSURE
Zheng, L.; Xu, W.; Liu, S.; Sun, W.; Li, J.H.; Zhou, H.; Qu, L.H.; Yang, J.H.
ENSURE: the encyclopedia of suppressor tRNA with an AI assistant
database
summary
Entrez Gene
Murphy, Terence D.; Brown, Garth; Hem, Vichet; Katz, Kenneth; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim; Maglott, Donna
Gene-centered information at NCBI
database
summary
Entrez Genomes
NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
database
summary
EnzEngDB
Yueming Long; et al.
Enzyme Engineering Database (EnzEngDB): A Platform for Sharing and Integrating Enzyme Engineering Data
database
summary
Enzyme Nomenclature
Gerard P. Moss
IUBMB Nomenclature Committee recommendations and updates
database
summary
EPD
Brenes, A, Afzal, V, Kent, R & Lamond A.I
The Encyclopedia of Proteome Dynamics (EPD)
database
summary
EpiDenovo
Mao, Fengbiao; Liu, Qi; Zhao, Xiaolu; Yang, Haonan; Guo, Sen; Xiao, Luoyuan; Li, Xianfeng; Teng, Huajing; Sun, Zhongsheng; Dou, Yali
No description supplied
database
summary
EpiFactors
Marakulina, Daria; Vorontsov, Ilya; Kulakovskiy, Ivan; Lennartsson, Andreas; DrablÃ¸s, Finn; Medvedeva, Yulia
Human epigenetic factors and complexes
database
summary
EpilepsyGene
Sun, Zhongsheng (contact); Ran, Xia; Li, Jinchen; Shao, Qianzhi; Chen, Huiqian; Lin, Zhongdong; Wu, Jinyu
Genes and mutations related to epilepsy
database
summary
Epitome
Schlessinger A.
1,2,3
, Ofran Y.
1,2
, Yachdav G.
1,2,3
and Rost B.
1,2,3
Database of structure-inferred antigenic epitopes
database
summary
eProS
Daniel Stockmann
Energy profiles of protein structures
database
summary
Equilibrator
Noor, Elad; Beber, Moritz; Gollub, Mattia; Mozaffari, Dana; Shebek, Kevin; Flamholz, Avi; Milo, Ron
eQuilibrator 3.0 â€“ a database solution for thermodynamic constant estimat
database
summary
eQuilibrator
Ron Milo
Thermodynamics calculator for biochemical reactions
database
summary
eRAM
Ni, Xin; Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Liang, Yunxiang; Guo, Dongming; Li, Xin; Tai, Jun; Chen, Geng'; Jin, Yaqiong; Liu, Zhimei; Shi, Tieliu
Rare diseases affect over a hundred million people worldwide, most of these
database
summary
ERGDB - Estrogen Responsive Genes Database
Estrogen responsive genes database
database
summary
ERGR
Ethanol-related genes in human and model organisms
database
summary
eRNAbase
Li, Chunquan; Song, Chao; Zhang, Guorui; Mu, Xinxin; Feng, Chenchen; Zhang, Qinyi; Song, Shuang; Zhang, Yuexin2; Yin, Mingxue; Zhang, Hang; Tang, Huifang
eRNAbaseï¼šA comprehensive database for decoding the regulatory eRNAs in human and mouse
database
summary
EROP-Moscow
Zamyatnin A.A, Borchikov A.S., Vladimirov M.G. and Voronina O.L.
A database of Endogenous Regulatory OligoPeptides
database
summary
ESC
Scaria, Vinod; Rophina, Mercy; Pandhare, Kavita; Shamnath, Afra; Imran, Mohamed; Jolly, Bani
SARS-CoV-2 immune escape variants
database
summary
ESE Finder
A database of yeast promoters
database
summary
Essential genes in E. coli [legacy]
First results of an
E. coli
gene deletion project
database
summary
euGenes
Gilbert, D.
Common summaries of gene and genomic information for eukaryotic organisms
database
summary
euHCVdb
European Hepatitis C Virus database
database
summary
Eukaryotic Promoter Database, EPD
Meylan, Patrick
;Dreos, RenÃƒÂ©
;Ambrosini, Giovanna
1,2
;Groux, Romain
1,2
;Bucher, Philipp
1,2
The Eukaryotic Promoter Database (EPD) provides accurate transcription star
database
summary
EukProt
Daniel Richter,
2,3
CÃƒÂ©dric Berney,
JÃƒÂ¼rgen Strassert,
Fabien Burki,
2,3
Colomban de Vargas
EukProt is a database of published and publicly available predicted protein
database
summary
euL1db
Cristofari, Gael; Mir, Ashfaq; Philippe, Claude
L1 retrotransposon insertions in humans
database
summary
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)
Liao, Jian-You;Yang, Bing;Zhang, Yu-Chan;Wang, Xiao-Juan;Ye, Yushan;Peng, Jing-Wen;Yang, Zhi-Zhi;He, Jie-Hua;Zhang, Yin;Hu, KaiShun;Lin, De-Chen;Yin, Dong
No description supplied
database
summary
EURISCO
Weise, Stephan; Oppermann, Markus; Maggioni, Lorenzo; van Hintum, Theo; KnÃƒÂ¼pffer, Helmut
European catalogue for plant genetic resources
database
summary
EURISCO
Weise, Stephan; Kotni, Pragna; van Hintum, Theo; Maggioni, Lorenzo; Oppermann, Markus
EURISCO update 2023: the European Search Catalogue for Plant Genetic Resour
database
summary
Europe PMC
Harrison, Melissa; Rosonovski, Summer; Levchenko, Maria; Bhatnagar, Rajat; Chandrasekaran, Umamageswari; Faulk, Lynne; Hassan, Islam; Ide-Smith, Michele; Jeffryes, Matthew; Mubashar, Syed Irtaza; Nassar, Maaly; Palanisamy, Madhumiethaa Jayaprabha; Parkin, Michael; Poluru, Jagadeeswararao; Rogers, Frances; Saha, Shyamasree; Selim, Mohamed; Shafique, Zunaira; Stephenson, David; Tirunagari, Santosh; Venkatesan, Aravind; Xing, Lijun
Europe PMC (https://europepmc.org) is a comprehensive resource of biomedica
database
summary
Europe PubMed Central
McEntyre, Johanna; KAFKAS, SENAY
European PubMed Central, archive of full-text papers
database
summary
European Genome-phenome Archive (EGA)
Lappalainen I, Almeida-King J, Kumanduri V, Marin-Garcia P and Flicek P
The European GenomeÃƒÂ¢Ã¢â€šÂ¬Ã¢â‚¬Å“phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects. The EGA contains data collected from individuals who have given consent for its use in research, but not for open public distribution.
database
summary
European Nucleotide Archive
Harrison, Peter; Ahamed, Alisha; Aslam, Raheela; Alako, Blaise; Burgin, Josephine; Buso, Nicola; Courtot, MÃƒÂ©lanie; Fan, Jun; Gupta, Dipayan; Haseeb, Muhammad; Holt, Sam; Ibrahim, Talal; Ivanov, Eugene; Jayathilaka, Suran; Balavenkataraman Kadhirvelu, Vish
All known nucleotide and protein sequences
database
summary
European Nucleotide Archive
Cochrane, G.; Alako, A.; Almeida, A.; Atienza-Herrero, J.; Avakov, S.; Ayadi, K.; et al.
All known nucleotide and protein sequences
database
summary
European rRNA database
All complete or nearly complete rRNA sequences
database
summary
EVA
Keane, Thomas; Cezard, Timothe; Cunningham, Fiona; Hunt, Sarah; Koylass, Baron; Kumar, Nithin; Saunders, Gary; Shen, April; Silva, Andres; Tsukanov, Kirill; Venkataraman, Sundar; Flicek, Paul; Parkinson, Helen
European Variation Archive
database
summary
EVAtlas
Guo, Anyuan; Liu, Chun-Jie; Xie, Gui-Yan; Miao, Yaru; Xia, Mengxuan; Wang, Yi; Lei, Qian; Zhang, Qiong
was EVmiRNA
database
summary
EVEREST - EVolutionary Ensembles of REcurrent SegmenTs
Portugaly E.
Linial N.
and Linial M.
Automatically generated protein domain families
database
summary
EVlncRNAs
Zhou, Yaoqi; Zhou, Bailing; Ji, Baohua; Shen, Congcong; Zhang, Xia; Yu, Xue; Huang, Pingping; Yu, Ru; Zhang, Hongmei; Dou, Xianghua; Chen, Qingshuai; Zeng, Qiangcheng; Wang, Xiaoxin; Cao, Zanxia; Hu, Guodong; Xu, Shicai; zhao, huiying; Yang, Yuedong.; Wan
EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments
database
summary
EVLncRNAs
Zhou, Yaoqi; Zhou, Bailing; Ji, Baohua; Liu, Kui; Hu, Guodong; Wang, Fei; Chen, Qingshuai; Yu, Ru; Huang, Pingping; Ren, Jing; Guo, Chengang; Zhao, Huiying2; Zhang, Hongmei; Zhao, Dongbo; Li, Zhiwei; Zeng, Qiangcheng; Yu, Jia-Feng; Bian, Yunqiang; Cao, Zanxia; Xu, Shicai; Yang, Yuedong.; Wang, Jihua
Long non-coding RNAs (lncRNAs) play important functional roles in various b
database
summary
EVmiRNA: a database of miRNA profiling in extracellular vesicles
Liu, Teng;Zhang, Qiong;Zhang, Jiankun;Li, Chao;Miao, Ya-Ru;Lei, Qian;Li, Qiubai;Guo, An-Yuan
No description supplied
database
summary
EVOG
Kim, D.-S.
, Cho, C.-Y.
, Huh, J-W.
, Kim, H.-S.
, Cho, H.-G.
A database for evolutionary analysis of overlapping genes
database
summary
Evola
Human genes and their vertebrate orthologs
database
summary
EWAS Open Platform
Bao, Yi-Ming; xiong, zhuang; Yang, Fei`; Li, Mengwei; Ma, Yingke; Zhao, Wei; Guoliang, Wang; Li, Zhaohua; Zheng, Xinchang; Zou, Dong; Wenting, Zong; Hongen, Kang; Jia, Yaokai; Li, Rujiao; Zhang, Zhang
Analysis platform for EWAS research
database
summary
ExAC browser
Karczewski, Konrad; Weisburd, Ben; Thomas, Brett; Ruderfer, Douglas; Kavanagh, David; Hamamsy, Tymor; Lek, Monkol; Samocha, Kaitlin; Cummings, Beryl; Birnbaum, Daniel; Consortium, Exome; Daly, Mark; MacArthur, Daniel
Exome sequence data from the Exome Aggregation Consortium
database
summary
ExoCarta
Suresh Mathivanan
, Cassie Patterson
, Gavin E. Reid
and Richard J. Simpson
Database on exosomes, membrane vesicles of endocytic origin released by diverse cell types
database
summary
ExoLocator
Khoo, Aik Aun; Ogrizek-TomaÅ¡, Mario; BuloviÄ‡, Ana; Korpar, Matija; GÃ¼rler, Ece; SlijepÄ\x8DeviÄ‡, Ivan; Å ikiÄ‡, Mile; Mihalek, Ivana
Protein-coding exons from completed verterbrate genomes
database
summary
Exome Aggregation Consortium
Exome Aggregation Consortium
61,486 unrelated exomes
database
summary
ExoRBase
Huang, Shenglin; Li, Shengli.; Li, Yuchen; Chen, Bing; Zhao, Jingjing; Yu, Shulin; Tang, Yuan; Zheng, Qiupeng; Wang, Peng; He, Xianghuo
No description supplied
database
summary
exoRBase
Huang, Shenglin; Lai, Hongyan; Li, Yuchen; Hu, Jia; Liao, Jiatao; Su, Ying; Li, Qin; Chen, Bing..; Zhang, Hena; Li, Caiping; Wang, Zhen"; Li, Yan ..; Wang, Jialei; Meng, Zhiqiang; Huang, Zhaohui
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicle
database
summary
ExplorEnz
Reference database of the IUBMB Enzyme Nomenclature
database
summary
Exposome-Explorer
Scalbert, Augustin; Neveu, Vanessa; Moussy, Alice; Rouaix, HÃƒÂ©loÃƒÂ¯se; Wedekind, Roland; Pon, Allison; Knox, Craig; Wishart, David
Biomarkers of exposure to disease risk factors
database
summary
Expression Atlas
Papatheodorou, Irene; George, Nancy; Madrigal, Pedro; Vathrakokoili Pournara, Anna; Prakash, Ananth; MuÃ±oz-Pomer Fuentes, Alfonso; Nolte, Nadja Francesca; Thanki, Anil; MarugÃ¡n, JosÃ©; Bi, Yalan; Iqbal, Haider; Kumbham, Upendra; Zhao, Lingyun; Fexova, Silv
Expression Atlas update: Insights from sequencing data at both bulk and single cell level
database
summary
Expression Atlas
Petryszak, Robert; Burdett, Tony; Fiorelli, Benedetto; Fonseca, Nuno; Gonzalez-Porta, Mar; Hastings, Emma; Huber, Wolfgang; Jupp, Simon; Keays, Maria; Kryvych, Nataliya; McMurry, Julie; Marioni, John; Malone, James; Megy, Karyn; Rustici, Gabriella; Tang, Amy; Taubert, Jan; Williams, Eleanor; Parkinson, Helen; Brazma, Alvis
Gene Expression Atlas
database
summary
Expression Atlas
Papatheodorou, Irene; Fonseca, Nuno; Keays, Maria; Tang, Amy; Barrera Casanova, Elisabet; Bazant, Wojciech; Burke, Melissa; FÃƒÂ¼llgrabe, Anja; MuÃƒÂ±oz-Pomer Fuentes, Alfonso; George, Nancy; Huerta Martinez, Laura; Koskinen, Satu; Mohammed, Suhaib; Geniza, Matthew; Preece, Justin; Jaiswal, Pankaj; Jarnuczak, Andrew; Huber, Wolfgang; Stegle, Oliver; Vizcaino, Juan Antonio; Brazma, Alvis; Petryszak, Robert
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that
database
summary
Expression Atlas
Papatheodorou, Irene; Moreno, Pablo; Fexova, Silvie; George, Nancy; Manning, Jonathan; Miao, Zhichao; Mohammed, Suhaib; MuÃ±oz-Pomer Fuentes, Alfonso; FÃ¼llgrabe, Anja; Bi, Yalan; Bush, Natassja; Iqbal, Haider; Kumbham, Upendra; Solovyev, Andrey; Zhao, Ling
Expression Atlas update: gene and protein expression in multiple species
database
summary
EXPRESSO
Yuliang Feng
The 3D genome, the epigenome and gene expression
database
summary
ExtraTrain
Tobes, R., Pareja, E., Pareja-Tobes, P., Manrique, M., Pareja-Tobes, E. Bonal, J.
Extragenic and Transcriptional information in prokaryotic organisms
database
summary
EyeSite
Families of proteins functioning in the eye
database
summary
EzCatDB
Nagano, Nozomi; Nakayama, Naoko; Ikeda, Kazuyoshi; Fukuie, Masaru; Yokota, Kiyonobu; Doi, Takuo; Kato, Tsuyoshi; Tomii, Kentaro
Enzyme Catalytic Mechanism Database
database
summary
F-SNP
Functional effects of various human SNPs
database
summary
Factorbook
Zhiping Weng
Human transcription factor binding data from ChIP-seq
database
summary
Factorbook
Weng, Zhiping; Pratt, Henry; Andrews, Gregory; Phalke, Nishigandha; Purcaro, Michael; van der Velde, Arjan; Moore, Jill
Factorbook: An updated catalog of transcription factor motifs and candidate
database
summary
FAIRDOMHub
Goble, Carole; Wolstencroft, Katherine; Krebs, Olga; Snoep, Jacky; Stanford, Natalie; Bacall, Finn; Golebiewski, Martin; Kuzyakiv, Rostyslav; Nguyen, Quyen; Owen, Stuart; Soiland-Reyes, Stian; Straszewski, Jakub; van Niekerk, Dawie; Williams, Alan; Malmstroem, Lars; Rinn, Bernd; MÃƒÂ¼ller, Wolfgang
Findable, Accessible, Interoperable and Reusable Data, Operating procedures and Models
database
summary
FANTOM
Kasukawa, Takeya; Abugessaisa, Imad; Ramilowski, Jordan; Lizio, Marina; Severin, Jessica; Hasegawa, Akira; Harshbarger, Jayson; Kondo, Atsushi; Noguchi, Shuhei; Yip, Chi Wai; Ooi, Jasmine Li Ching; Tagami, Michihira; Hori, Fumi; Agrawal, Saumya; Hon, Chun
Functional annotation of mouse full-length cDNA clones
database
summary
FARME DB
James C. Wallace, Jesse A. Port, Marissa N. Smith, and Elaine M. Faustman
Functional Antibiotic Resistance Metagenomic Element Database
database
summary
FAVOR
Daofeng Li; et al.
Impact of Genetic Variations on Functional Genomes (FAVOR) version 2.0
database
summary
FAVOR
Zhou, Hufeng; Verma, Vineet; Li, Xihao; Li, Zilin; Shedd, Nicole; Li, Thomas C; Yang, Haoyu; Zhang, Alvin; Borsari, Beatrice; Buyske, Steven; Gerstein, Mark; Matise, Tara; Zody, Mike; Neale, Benjamin; Weng, Zhiping; Sunyaev, Shamil R; Lin, Xihong
Functional Annotation of Variants - Online Resource
database
summary
FCP
GarcÃƒÂa-Serna R., Opatowski L. and Mestres J.
Functional coverage of the proteome by enzyme structures
database
summary
FerrDb
Nan Zhou, Li Peng, Qiqi Luo, Tong Yin, Huiran Sun, Yuhong Zhang, Xiaolei Shi, Xian Peng, Jinku Bao, Yuping Ning, Xiaoqing Yuan
Ferroptosis regulators
database
summary
FGDB
Gueldener U.
1,3
, Mannhaupt G.
, Muensterkoetter M.
, Haase D.
, Oesterheld M.
, Stuempflen V.
, Mewes H.W.
1,3
and Adam G.
Plant pathogen
Fusarium graminearum
genome database
database
summary
FINDbase
Patrinos, George; Papadopoulos, Petros; Viennas, Emmanouil; Gkantouna, Vassiliki; Pavlidis, Cristiana; Bartsakoulia, Marina; Ioannou, Zafeiria-Marina; Ratbi, Ilham; Sefiani, Abdelaziz; Tsaknakis, John; Poulas, Konstantinos; Tzimas, Giannis
Frequencies of INherited Disorders: Pathogenic mutation frequencies worldwide
database
summary
FireDB
Tress, Michael; Maietta, Paolo; Lopez, Gonzalo; Carro, Angel; Leon, Leticia; Pingilley, Benjamin; Valencia, Alfonso
Functionally Important REsidues in protein structures
database
summary
FireProtDB
Bednar, David; Stourac, Jan; Dubrava, Juraj; Musil, Milos; Horackova, Jana; Damborsky, Jiri; Mazurenko, Stanislav
Protein stability data
database
summary
FL-circAS
Chuang, Trees-Juen; Chiang, Tai-Wei; Jhong, Song-En; Chen, Yu-Chen; Chen, Chia-Ying; Wu, Wei-Sheng
FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing
database
summary
FlavorDB
Bagler, Ganesh; Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; NK, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi
All known flavor molecules, their flavor profiles, and chemical descriptors
database
summary
FLIBase
He, Xianghuo; Shi, Qili; Li, Xinrong; Liu, Yizhe; Chen, Zhiao
FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues
database
summary
FLOR-ID
PÃƒÂ©rilleux, Claire; BouchÃƒÂ©, FrÃƒÂ©dÃƒÂ©ric; Lobet, Guillaume; Tocquin, Pierre
Flowering Interactive Database
database
summary
FlyAtlas
David Leader
FlyAtlas: the
Drosophila
gene expression atlas
database
summary
FlyAtlas 2
Leader, David; Krause, Sue; Overend, Gayle; Dow, Julian
FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression
database
summary
FlyAtlas 2
No description supplied
database
summary
FlyBrain
Database of the
Drosophila
nervous system
database
summary
FlyEx
Atlas of the spatiotemporal expression of segmentation genes in
Drosophila
database
summary
FlyFactorSurvey
Lihua Julie Zhu
1,2
, Ryan G. Christensen
, Majid Kazemian
, Christopher J. Hull
, Metewo Selase Enuameh
, Matthew D. Basciotta
, Jessie A. Brasefield
, Cong Zhu
, Yuna Asriyan
, David S. Lapointe
, Saurabh Sinha
4,6
, Scot A. Wolfe
1,7
and Michael H. Brodskyp
1,2
Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
database
summary
FlyMine
Lyne R., Burns G., Mata J., Penkett C.J., Rustici G., Chen D., Langford C., Vetrie D. and Bahler J.
An integrated database for Drosophila and Anopheles genomics
database
summary
FlyRNAi
Hu, Yanhui; Comjean, Aram; Rodiger, Jonathan; Liu, Yifang; Gao, Yue; Chung, Verena; Zirin, Jonathan; Perrimon, Norbert; Mohr, Stephanie
The Drosophila RNAi Screening Center Database
database
summary
FLYSNP
SNP data for Drosophila melanogaster
database
summary
FlyTF
Pfreundt, U.
1,2
, James, D.
, Tweedie, S.
, Wilson, D.
, Teichmann, S.
, and Adryan, B.
1,2
Drosophila transcription factors
database
summary
FlyTrap
Drosophila
transgenic lines created using an intron protein trap strategy
database
summary
ForestTreeDB
Pavy N.
, Johnson J.
, Crow J.
, Paule C.
, Kunau T.
, MacKay J.
and Retzel E.
Annotated ESTs from diverse organs of spruce, pine and poplar
database
summary
fPOP
Yan Yuan Tseng, Z. Jeffrey Chen, and Wen-Hsiung Li
Footprinting protein functional surfaces by comparative patterns
database
summary
FragmentStore
Jessica Ahmed
, Catherine L. Worth
, Paul Thaben
, Christian Matzig
, Corinna Blasse
, Mathias Dunkel
and Robert Preissner
Comprehensive database of fragments linking metabolites, toxic molecules and drugs
database
summary
fRNAdb
Functional RNA Database
database
summary
FunCoup
Sonnhammer, Erik L.L.; Schmitt, Thomas; Ogris, Christoph
Networks of functional coupling
database
summary
FunCoup
Sonnhammer, Erik; Ogris, Christoph; Kaduk, Mateusz; Guala, Dimitri,
This release of the FunCoup database (http://funcoup.sbc.su.se) is the four
database
summary
Fungal Genome Size Database
Kullman, B.
, Tamm, H.
1,2
and Kullman, K.
Genome sizes of various fungi
database
summary
Fungal Names
Wu, Linhuan; Wang, Fang; Wang, Ke; Cai, Lei; Zhao, Mingjun; Kirk, Paul M.; Fan, Guomei; Sun, Qinglan; Li, Bo; Wang, Shuai; Yu, Zhengfei; Han, Dong; Ma, Juncai; Yao, Yijian
Fungal taxonomy
database
summary
FungiDB
Jason Stajich
Functional genomics of fungi
database
summary
FunShift
Functional divergence between the subfamilies of a protein domain family
database
summary
FunSimMat
Gene Ontology-based functional similarity values for proteins and protein families
database
summary
FunTree
Nicholas Furnham
Evolution of novel enzyme functions in enzyme superfamilies
database
summary
FusariumDB
Bongsoo Park, Jongsun Park, Kyeong-Chae Cheong, Jaeyoung Choi, Kyongyong Jung, Donghan Kim, Yong-Hwan Lee, Todd J. Ward, Kerry O'Donnell, David M. Geiser, and Seogchan Kang
Comparative genomics of Fusarium strains
database
summary
FusionCancer
Wang Y, Wu N, Liu J, Wu Z, Dong D
FusionCancer - a database of cancer fusion genes derived from RNA-Seq data
database
summary
FusionDB
Mahlich, Yannick; Zhu, Chengsheng; Miller, Carl; Bromberg, Yana
No description supplied
database
summary
FusionGDB
Kim, Pora; Tan, Hua; Liu, Jiajia; Lee, Haeseung ,; Jung, Hyesoo; Kumar, Himansu; Zhou, Xiaobo
FusionGDB 2.0: fusion gene annotation updates aided by deep learning
database
summary
FusionNeoAntigen
Kim, Pora; Kumar, Himansu; Luo, Ruihan; Wen, Jianguo; Yang, Chengyuan; Zhou, Xiaobo1
FusionNeoAntigen: a resource of Fusion gene-specific Neoantigens
database
summary
FusionPDB
Kim, Pora; Kumar, Himansu; Tang, Lin-Ya; Yang, Chengyuan
FusionPDB: a knowledgebase of human Fusion Proteins
database
summary
FuzDB
Fuxreiter, Monika; Hatos, AndrÃ¡s; Monzon, Alexander; Tosatto, Silvio; Piovesan, Damiano
FuzDB: a new phase in understanding fuzzy interactions
database
summary
FuzDB
Fuxreiter, Monika; Miskei, Marton; Antal, Csaba
Fuzzy Complexes Database
database
summary
G protein research platform
Gloriam, David; PÃ¡ndy-Szekeres, GÃ¡spÃ¡r; Esguerra, Mauricio; Hauser, Alexander; Caroli, Jimmy; Munk, Christian; Pilger, Steven; KeserÅ±, GyÃ¶rgy; Kooistra, Albert
G proteins and their interactions
database
summary
GÉnoPlante-Info
Samson, D., Legeai, F., Karsenty, E., Reboux, S., Veyrieras, J.-B., Just, J., Barillot, E.
Plant genomic data derived from the GÉnoplante consortium
database
summary
G2Cdb
Genes to Cognition
database
summary
G4Atlas
Yu, Haopeng; Qi, Yiman; Yang, Bibo; Yang, Xiaofei; Ding, Yiliang
Experimentally determined RNA G-quadruplexes in transcriptomes
database
summary
G4LDB
Qian Li
G-quadruplex Ligands Database
database
summary
G4LDB
Yang, Shu; Wang, Yu-huan; Yang, Qianfan; Lin, Xiao; Chen, Die; Wang, Zhi-yin; Chen, Bin; Han, Hua-Yi; Chen, Hao-Di; Cai, Kai-Cong; Li, Qian..; Li, Feng ,`; Tang, Yalin
G-quadruplexes and ligands
database
summary
GABI-Kat SimpleSearch database
Weisshaar, Bernd; Kleinboelting, Nils; Huep, Gunnar; Kloetgen, Andreas; Viehoever, Prisca
T-DNA insertions in
Arabidopsis
, their flanking sequence tags
database
summary
GabiPD
RiaÃƒÆ’Ã‚Â±o-PachÃƒÆ’Ã‚Â³n, D.M.
1,2
, Nagel, A.
, Neigenfind, J.
, Wagner, R.
, Basekow, R.
, Weber, E.
, Mueller-Roeber, B.
, Diehl, S.
, and Kersten, B.
1,2
A plant integrative 'omics' database
database
summary
GadFly
Genome annotation database of
Drosophila
database
summary
GAIA
Ouangraoua, Aida; Vannutelli, Anais; Schell, Lauriane; Perreault, Jean-Pierre
Predicted G-quadruplexes in genomes and transcriptomes
database
summary
Gallus Gbrowse
Genomic information on chicken and other avian species
database
summary
GBshape
Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley; Parker, Stephen CJ; Nuzhdin, Sergey; Tullius, Thomas; Rohs, Remo
Genome Browser for DNA shape annotations
database
summary
GCM and gcType
Wu, Linhuan; Shi, Wenyu; Sun, Qinglan; Fan, Guomei; Sugawara, Hideaki; Ohkuma, Moriya; Itoh, Takashi; Zhou, Yuguang; Cai, Man; Kim, Song-Gun; Lee, Jung-Sook; Sedlacek, Ivo; Arahal, David; Lucena, Teresa; Kawasaki, Hiroko; Evtushenko, Lyudmila; Weir, Bevan
WDCM 10K sequencing projects
database
summary
gcPathogen
Wu, Linhuan; Guo, Chongye; Chen, Qi; Fan, Guomei; Sun, Yan; Nie, Jingyi; Li, Shiwen; Wang, Shuai; Meng, Zhen; Zhou, Yuanchun; Shen, Zhihong; Ma, Juncai; Sun, Qinglan
gcPathogen: a comprehensive genomic resource of human pathogens for public health
database
summary
GDP
Jian Ren
Biomedical graphics
database
summary
GDPF
Zhang, Zheng; Pan, Zhuo; Li, Dan-dan; Li, Peng; Geng, Yu; Jiang, Yiru; Liu, Ya; Li, Yue-zhong
GDPF: a data resource for the distribution of prokaryotic protein families across the global biosphere
database
summary
GDSC
Mathew Garnett
Genomics of Drug Sensitivity in Cancer: Sensitivity for anti-cancer drugs in various cell lines
database
summary
GEAR
Motomu Endo; et al.
GEAR: Genomic and Evolutionary Analysis Resource for Arabidopsis thaliana
database
summary
GEISHA
Antin, Parker B; Yatskievych, Tatiana; Davey, Sean; Darnell, Diana
Gallus
expression
in situ
hybridization analysis
database
summary
GELBANK
Babnigg G., Giometti C.S.
2D gel electrophoresis patterns from completed genomes
database
summary
GEM2Net
Zaag, Rim; Tamby, Jean; Guichard, CÃƒÂ©cile; Tariq, Zakia; Rigaill, Guillem; Delannoy, Etienne; Renou, Jean; Balzergue, Sandrine; Mary-Huard, Tristan; Aubourg, SÃƒÂ©bastien; Martin-Magniette, Marie; Brunaud, VÃƒÂ©ronique
Arabidopsis thaliana
genes involved in stress response
database
summary
GeMInA
Lynn M. Schriml
, Cesar Arze
, Suvarna Nadendla
, Anu Ganapathy
, Victor Felix
, Anup Mahurkar
, Katherine Phillippy
, Aaron Gussman
1,2
, Sam Angiuoli
, Elodie Ghedin
, Owen White
and Neil Hall
Genomic Metadata for Infectious Agents
database
summary
GenBank
Sayers, Eric; Cavanaugh, Mark; Clark, Karen; Pruitt, Kim; Sherry, Stephen; Karsch-Mizrachi, Ilene
All known nucleotide and protein sequences
database
summary
GenBank
Sayers, Eric; Cavanaugh, Mark; Clark, Karen; Pruitt, Kim; Sherry, Stephen; Yankie, Linda; Karsch-Mizrachi, Ilene
GenBank 2024 Update
database
summary
GenBank
Sayers, Eric; Cavanaugh, Mark; Clark, Karen; Pruitt, Kim; Sherry, Stephen; Yankie, Linda; Karsch-Mizrachi, Ilene
Genbank
database
summary
GenCC Database
The Gene Curation Coalition Database
database
summary
GENCODE
Frankish, Adam ; Carbonell, Silvia; Diekhans, Mark; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M.; Sisu, Cristina; Wright, James; Arnan, Carme; Banerjee, Abhimanyu; Barnes, If; Bennett, Ruth; Berry, Andrew.; Bignell, Alexandra; Boix, Carles; Calvet
GENCODE: reference annotation for the human and mouse genomes in 2023
database
summary
GenColors
Marius Felder
Genome annotation and comparison database for smaller genomes
database
summary
GenDiS
Genomic distribution of protein structural superfamilies
database
summary
Gene Expression Barcode
McCall, Matthew; Jaffee, Harris; Zelisko, Susan; Sinha, Neeraj; Hooiveld, Guido; Irizarry, Rafael; Zilliox, Michael
Gene expression data sorted into two groups: expressed and not expressed genes
database
summary
Gene Expression Nebulas
Zhang, Zhang; Zhang, Yuansheng; Zou, Dong; Zhu, Tongtong; Xu, Tianyi; Chen, Ming; Niu, Guangyi; Wenting, Zong; Pan, Rong; Jing, Wei; Sang, Jian; Liu, Chang; Xiong, Yujia; Sun, Yubin; Zhai, Shuang; Chen, Huanxin; Zhao, Wen-Ming; Xiao, Jingfa; Bao, Yi-Ming;
Expression profiles across species, bulk and single cell
database
summary
Gene Ontology
Albou, Laurent-Philippe; Thomas, Paul; Mungall, Chris; Blake, Judith; Sternberg, Paul; Cherry, J. Michael; Gaudet, Pascale; Van Auken, Kimberly; Hill, David P; Carbon, Seth; Mi, Huaiyu'; Aleksander, Suzi
Gene Ontology Database
database
summary
Gene Wiki
Jon W. Huss III, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch, and Andrew I. Su
An informal collection of pages on human genes
database
summary
Gene3D
Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.
Precalculated structural assignments for whole genomes
database
summary
Gene3D
Lees, Jonathan; Lewis, Tony; Sillitoe, Ian; Dawson, Natalie; Lam, Su Datt; Das, Sayoni; Clarke, Tristan; Lee, David; Orengo, Christine
No description supplied
database
summary
GeneAnnot
Chalifa-Caspi, V., Shmueli, O., Shmoish, M., Shklar, M.,Rosen, N., Benjamin-Rodrig, H., Yanai, I., Ophir, R., Iny Stein, T., Kats, P., Almashanu, L., Safran, M., Lancet, D.
Revised and improved annotation of Affymetrix human gene probe sets
database
summary
GENEasso
Tingjun Hou; et al.
GENEasso: an integrated resource for gene-phenotype and gene-disease associations
database
summary
GeneCards
Safran, M., Shmueli, O., Rosen, N., Shmoish, M., Shklar, M., Benjamin-Rodrig, H., Almashanu, L., Chalifa-Caspi, V., Lancet, D.
Integrated database of human genes, maps, proteins, and diseases
database
summary
GeneDB
The GeneDB Team
Curated database for protozoan and bacterial genomes sequenced at the Sanger Centre
database
summary
GeneFamily
Shuai Cheng Li; et al.
GeneFamily: a comprehensive mammalian gene family database with extensive functional annotations
database
summary
GeneFriends
de MagalhÃ£es, JoÃ£o Pedro; Raina, Priyanka; Guinea, Rodrigo; Chatsirisupachai, Kasit; De Almeida Lopes, Ines; Farooq, Zoya; Guerra, Cristina; Solyom, Csaba
GeneFriends: Gene co-expression databases and tools for humans and model or
database
summary
GeneFriends
de MagalhÃƒÂ£es, JoÃƒÂ£o Pedro; van Dam, Sipko; Craig, Thomas
RNAseq based human gene and transcript co-expression map
database
summary
GeneLoc
Rosen, N., Chalifa-Caspi, V., Shklar, M., Almashanu, L., Safran, M., Lancet, D.
Gene Location database, formerly known as Unified database for human genome mapping (UDB)
database
summary
GeneNest
Gene indices of human, mouse, zebrafish,
Arabidopsis
, and
Drosophila
database
summary
GeneNet
Ananko, E.A., Podkolodny, N.L., Stepanenko, I.L., Podkolodnaya, O.A., Rasskazov, D.A., Miginsky, D.S., Likhoshvai, V.A., Ratushny, A.V., Podkolodnaya, N.N., Kolchanov, N.A.
Database on gene network components
database
summary
GeneNote
Shmueli, O., Shmoish, M., Rosen, N., Benjamin-Rodrig, H., Yanai, I., Ophir, R., Shklar, M., Almashanu, L., Madi, A., Sirota, A., Kats, P., Chalifa-Caspi, V., Safran, M., Lancet, D.
Human genes expression profiles in healthy tissues
database
summary
GenePaint
Gene expression patterns in the mouse
database
summary
GeneSigDB
Baker, Erich; Jay, Jeremy; Bubier, Jason; Langston, Michael; Chesler, Elissa
Gene Signature DataBase
database
summary
GEneSTATION
Rokas, Antonis ; Kim, Mara; Cooper, Brian; Venkat, Rohit; Phillips, Julie; Eidem, Haley; Hirbo, Jbril; Nutakki, Sashank; Williams, Scott; Muglia, Louis; Capra, John; Petren, Kenneth; Abbot, Patrick; McGary, Kriston
Evolutionary genomics of pregnancy-related tissues and phenotypes
database
summary
Genetic Codes
Deviations from the standard genetic codes in various organisms and organelles
database
summary
Genetics Home Reference
A general guide on human hereditary diseases
database
summary
GeneTrap
Expression patterns in an embryonic stem library of gene trap insertions
database
summary
GeneWeaver
Erich Baker
Functional genomics analysis system
database
summary
GenoBase
Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Kouichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Nomura, Wataru; Suharnan, Sivasundaram; Nakayashiki, Toru; Aref, Walid; Gribskov, Michael; Tohsato, Yukako,; Bochner, Barry; Kihara, Daisuke; Conway, Tyrrell; Wanner, Barry; Mori, Hirotada
Escherichia coli K-12 in-frame, single-gene knockout mutants
database
summary
GenoList
An integrated environment for comparative analysis of microbial genomes
database
summary
Genome Database for Rosaceae
Main, Dorrie; Jung, Sook; Ficklin, Stephen; Lee, Taein; Cheng, Chun-Huai; Blenda, Anna; Zheng, Ping; Yu, Jing; Bombarely, Aureliano; Cho, Il-Hyung; Yu, Sushan; Evans, Katherine; Peace, Cameron; Abbott, Albert; Mueller, Lukas; Olmstead, Mercy
Genetics and genomics data on apple, cherry, peach, pear, raspberry, rose and strawberry
database
summary
Genome Project Database
Klimke W., Kochergin A., Landrum M., Pruitt K., Resenchuk S., Sermrann P. and Tatusova T.
NCBI's database of large-scale genome sequencing projects
database
summary
Genome Reviews
Kersey P.
, Bower L.
, Morris L.
, Horne A.
, Petryszak R.
, Kanz C.
, Kanapin A.
, Das U.
, Mulder N.
, Pruess M.
, Duggan K.
, Quevillon E.
, McLaren P.
, Kulikova T.
, Faruque N.
, Whitfield E.
, Duret L.
, Penel S.
, Reuter I.
, Zhu W.
and Apweiler R.
Integrated view of complete genomes
database
summary
Genome3D
Lewis, Tony; Sillitoe, Ian; Andreeva, Tony; Blundell, Tom; Buchan, Daniel; Chothia, Cyrus; Cozzetto, Domenico; Dana, JosÃ©; Filippis, Ioannis; Gough, Julian; Jones, David T; Kelley, Lawrence; Kleywegt, Gerard; Minneci, Federico; Murzin, Alexey; Ochoa, Bernardo; Oates, Matt; Punta, Marco; Rackham, Owen J; Stahlhacke, Jonathan; Sternberg, Michael; Velankar, Sameer; Mistry, Jaina
Domain structure predictions and 3D models for proteins from model genomes
database
summary
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation
Sillitoe, Ian;Andreeva, Antonina;Blundell, Tom L;Buchan, Daniel W A;Finn, Robert D;Gough, Julian;Jones, David;Kelley, Lawrence A;Paysan-Lafosse, Typhaine;Lam, Su Datt;Murzin, Alexey G;Pandurangan, Arun Prasad;Salazar, Gustavo A;Skwark, Marcin J;Sternberg, Michael J E;Velankar, Sameer;Orengo, Christine
No description supplied
database
summary
GenomeAtlas
Hallin, P.F., Jensen, L.J., Skovgaard, M., StÆrfeldt, H.H., Worning, P. and Ussery, D.W.
DNA structural properties of sequenced genomes
database
summary
GenomeCRISPR
Boutros, Michael; Rauscher, Benedikt; Heigwer, Florian; Breinig, Marco; Winter, Jan
High-throughput screening using the CRISPR/Cas-9 system
database
summary
GenomeRNAi
Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., and Boutros, M.
Cell-based RNAi phenotypes database
database
summary
Genomes OnLine Database (GOLD)
Mukherjee Supratim; Stamatis Dimitri; Bertsch Jon; Ovchinnikova Galina; Sundaramurthi Jagadish Chandrabose; Lee Janey; Kandimalla Mahathi; Chen I-Min A; Kyrpides Nikos C; Reddy T.B.K
The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manuall
database
summary
GenomeTraFaC
Jegga A.G.
1,2
, Chen J.
1,3
, Gowrisankar S.
1,3
, Deshmukh M.A.
, Gudivada R.
1,3
, Kong S.
, Kaimal V.
1,3
and Aronow B.J.
1,2,3
Conserved regulatory elements of human and mouse genes
database
summary
Genomic Threading Database
Structural annotations of complete genomes
database
summary
GenomicKB
Liu, Jie; Feng, Fan; Tang, Feitong; Gao, Yijia; Zhu, Dongyu; Li, Tianjun; Yang, Shuyuan; Yao, Yuan; Huang, Yuanhao
Knowledge Graph for the Human Genome
database
summary
Genomicus
Louis, Alexandra; Nguyen, Nga Thi Thuy; Vincens, Pierre; dufayard, jean-franÃ§ois; ROEST CROLLIUS, Hugues
Genomicus 2022: 12th anniversary â€“ Comparative tools for thousands of gen
database
summary
Genomicus
Louis, Alexandra; Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues
No description supplied
database
summary
Genomicus
Louis, Alexandra; Nguyen, Nga Thi Thuy; Muffato, Matthieu; Roest Crollius, Hugues
Syntenic relationships between eukaryote genomes
database
summary
GENSAT
Gene Expression Nervous System ATlas
database
summary
GEO
Clough, Emily; Barrett, Tanya; Wilhite, Stephen; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly; Phillippy, Katherine; Sherman, Patti; Lee, Hyeseung; Zhang, Naigong; Serova, Nadezhda; Wagner, Lukas; Zalunin, Vadi
NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
database
summary
GEO - Gene Expression Omnibus
Public gene expression repository
database
summary
Gephebase
Courtier-Orgogozo, Virginie, Martin, Arnaud
Gephebase is a manually-curated database compiling our accumulated knowledg
database
summary
GermOnline
Primig, M.
Expression data for the mitotic and meiotic cell cycle and gametogenesis in yeast and higher eukaryotes
database
summary
GermSAGE [Discontinued]
vul@od.nih.gov
SAGE data on gene expression in male germ cell development
database
summary
GESS
Wan, Jun; Fang, Shuyi; Li, Kailing; Shen, Jikui; Liu, Sheng; LIU, JULI; Yang, Lei; Hu, Chang-Deng
Global Evaluation of SARS-CoV2 Sequences
database
summary
GETPrime
Deplancke, Bart; David, Fabrice; Rougemont, Jacques
Gene- or transcript-specific primers for qPCR
database
summary
GiardiaDB.org
Genome resources for anaerobic pathogens Trichomonas vaginalis and Giardia lamblia
database
summary
GigaDB
GigaDB primarily serves as a repository to host data and tools associated w
database
summary
GIMICA
J. Tang, X. L. Wu, M. J. Mou, C. Wang, L. D. Wang, F. C. Li, M. Y. Guo, J. Y. Yin, W. Q. Xie, X. N. Wang, Y. X. Wang, Y. B. Ding, W. W. Xue, F. Zhu
Host Genetic and Immune Factors Shaping Human Microbiota
database
summary
GISSD
Group I Intron Sequence and Structure Database
database
summary
GLIDA
GPCR-Ligand Database
database
summary
Glycan
Carbohydrate database, part of the KEGG system
database
summary
Glycan Fragment DB
Wonpil Im
Database of glycan 3D structures
database
summary
Glycoconjugate Data Bank
Annotated structures of glycan molecules
database
summary
GlycoMapsDB
Conformational maps of disaccharides
database
summary
GlycomeDB
RenÃƒÆ’Ã‚Â© Ranzinger, Stephan Herget, Claus-Wilhelm von der Lieth, and Martin Frank
Carbohydrate structures
database
summary
GlycoPOST
Okuda, Shujiro; Watanabe, Yu; Aoki-Kinoshita, Kiyoko; Ishihama, Yasushi
Raw Mass Spectrometry glycomics data
database
summary
GlycoRNADB
Zheng, L.L.; Li, J.H.; Liu, S.; Sun, W.J.; Yang, J.H.; Qu, L.H.
GlycoRNADB: A Database of Glycorna Sequences, Structures, Abundance and Functions
database
summary
GlyTouCan
Aoki-Kinoshita, Kiyoko; Fujita, Akihiro; Aoki, Nobuyuki; Shinmachi, Daisuke; Matsubara, Masaaki; Tsuchiya, Shinichiro; Shiota, Masaaki; Ono, Tamiko; Yamada, Issaku
International Glycan Structure Repository
database
summary
GMRepo
Chen, Weihua; Dai, Die; Zhu, Jiaying; Sun, Chuqing; Li, Min; Liu, Jinxin; Wu, Sicheng; Ning, Kang; He, Lijie; Zhao, Xing-Ming
GMrepo v2: a curated human gut microbiome database with special focus on di
database
summary
GO
Thomas, Paul; et al.
THE GENE ONTOLOGY KNOWLEDGEBASE IN 2026
database
summary
GOA
Huntley, Rachael; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria; O'Donovan, Claire
Gene ontology annotation in UniProt
database
summary
GoFCards
Jinchen Li
Known and predicted gain-of-function variants
database
summary
GOLD
Reddy, TBK; Mukherjee, Supratim; Stamatis, Dimitrios; Li, Cindy; Ovchinnikova, Galina; Bertsch, Jon; Sundaramurthi, Jagadish Chandrabose; Kandimalla, Mahathi; Nicolopoulos, Paul; Favognano, Alessandro; Chen, I-Min; Kyrpides, Nikos
Twenty-Five Years of Genomes OnLine Database (GOLD): Data Updates and New F
database
summary
GOLD.db - Genomics Of Lipid-associated Disorders
Hackl, H., Trost, E., Maurer, M., Hartler, J., Mlecnik, B., Miranda-Saavedra, D., Stocker G., Trajanoski, Z.
Genes, proteins, and pathways implicated in lipid- associated disorders
database
summary
GoMapMan
RamÃ…Â¡ak, Ã…Â½iva; Ã…Â pela, Baebler; Rotter, Ana; Korbar, Matej; Mozeti?, Igor; Usadel, BjÃƒÂ¶rn; Gruden, Kristina
Unified plant-specific gene ontology
database
summary
GONUTS
Jim Hu
Gene Ontology Normal Usage Tracking System
database
summary
GotEnzymes
Nielsen, Jens; Li, Feiran; Chen, Yu; Anton, Mihail
Predicted enzyme kinetic parameters
database
summary
GPCR NaVa database
A database of natural sequence variants within the family of human G Protein-Coupled Receptors
database
summary
GPCRdb
Gloriam, David; Kooistra, Albert; Mordalski, Stefan; PÃƒÂ¡ndy-Szekeres, GÃƒÂ¡spÃƒÂ¡r; Esguerra, Mauricio; Mamyrbekov, Alibek; Munk, Christian; KeserÃ…Â±, GyÃƒÂ¶rgy
G protein-coupled receptors are the most abundant mediators of both human s
database
summary
GPCRdb
PÃ¡ndy-Szekeres, GÃ¡spÃ¡r; Caroli, Jimmy; Mamyrbekov, Alibek; Kermani, Ali; KeserÅ±, GyÃ¶rgy; Kooistra, Albert; Gloriam, David
GPCRdb in 2023: State-specific structure models using AlphaFold2 and new li
database
summary
gpDB - G-protein database
G-proteins and their interaction with GPCRs
database
summary
GPEdit
Han, Leng; Ruan, Hang; Li, Qiang; Liu, Yuan; Liu, Yaoming; Lussier, Charles; Diao, Lixia
A-to-I RNA editing in cancer
database
summary
GproteinDB
Gloriam, David; Taracena Herrera, Luis; PÃ¡ndy-Szekeres, GÃ¡spÃ¡r; Caroli, Jimmy; Kermani, Ali; Kulkarni, Yashraj; KeserÃ¼, GyÃ¶rgy
GproteinDb in 2024: G protein-GPCR AlphaFold2-Multimer models and interfaces
database
summary
GPSAdb
Guo, Shipeng; Xu, Zhougeng; Dong, Xiangjun; Hu, Dongjie; Jiang, Yanshuang; Wang, Qunxian; Zhang, Jie; Zhou, Qian; Liu, Shengchun; Song, Weihong
Genetic Perturbation Similarity Analysis
database
summary
GPX-Macrophage Expression Atlas
Grimes G., Moodie S., Beattie J.S., Craigon M., Dickinson P., Forster T., Livingston A., Mewissen M., Robertson K.A., Ross A.J., Sing G. and Ghazal P.
Gene expression in macrophages
database
summary
GrainGenes
Molecular and phenotypic information on wheat, barley, rye, triticale, and oats
database
summary
Gramene
Ware, Doreen; et al.
Gramene 2025: expanded comparative genomics and pathway resources, and a new community data submission tool
database
summary
Gramene
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
A resource for comparative grass genomics
database
summary
Gramene
Ware, Doreen; Tello-Ruiz, Marcela; Naithani, Sushma; Gupta, Parul; Olson, Andrew J; Wei, Sharon; Preece, Justin; Jiao, Yinping; Wang, Bo, .; Chougule, Kapeel; Garg, Priyanka; Elser, Justin; Kumari, Sunita; Kumar, Vivek; Contreras Moreira, Bruno; Naamati,
Gramene (http://www.gramene.org) is a phylogenomic resource for plants, bui
database
summary
GRAND
Quackenbush, John; Ben Guebila, Marouen; Lopes-Ramos, Camila; Weighill, Deborah; Sonawane, Abhijeet; Burkholz, Rebekka; Shamsaei, Behrouz; Platig, John; Glass, Kimberly; Kuijjer, Marieke
Human gene regulation models
database
summary
GRASP
GWAS results
database
summary
GreeNC
Aiese Cigliano, Riccardo; Di Marsico, Marco; PaytuvÃ, Andreu; Sanseverino, Walter
GreeNC 2.0: a comprehensive database of plant lncRNA
database
summary
GreeNC
PaytuvÃ, Andreu; Hermoso Pulido, Antonio; Anzar, Irantzu; Sanseverino, Walter; Aiese Cigliano, Riccardo
Green Non-Coding: lncRNAs in nine plant species
database
summary
Greengenes
DeSantis T.Z.
, Hugenholtz P.
, Larsen N.
, Rojas M.
, Brodie E.L.
, Keller K.
, Huber T.
, Dalevi D.
, Hu P.
and Andersen G.L.
A database of chimera-checked prokaryotic 16S rRNA genes
database
summary
GreenPhylDB
Rouard, Mathieu; Guignon, Valentin; Toure, Abdel; Droc, Gaetan; dufayard, jean-franÃƒÂ§ois; Conte, Matthieu
Comparative genomics of rice and Arabidopsis thaliana
database
summary
Greglist
G-quadruplex motifs and potentially G-quadruplex regulated genes
database
summary
GRNdb
Chen, Geng; Fang, Li; Li, Yunjin; Ma, Lu; Xu, Qiyue; Tan, Fei
TF-target relationsips inferred from single cell and bulk RNA-seq datasets
database
summary
GRSDB
Kostadinov R., Malhotra N., Viotti M., Shine R., DÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢Antonio L. and Bagga P.
Quadruplex forming 'G'-rich sequences in mammalian pre-mRNA
database
summary
GSRS
Southall, Noel; Peryea, Tyler; Miller, Mitchell; Katzel, Daniel; Anderson, Niko; Neyra, Jorge; Stemann, Sarah; Nguyen, Dac-Trung; Amugoda, Dammika; Newatia, Archana; Ghazzaoui, Ramez; Johanson, Elaine; Diederik, Herman; Callahan, Lawrence; Switzer, Frank
Global Substance Registration System
database
summary
GTDB
Parks, Donovan; Chuvochina, Maria; Rinke, Christian; Mussig, Aaron; Chaumeil, Pierre-Alain; Hugenholtz, Philip
Genome Taxonomy Database
database
summary
GTO
Jianbo Pan
Gene Therapy Omnibus
database
summary
GTOP - Genomes To Protein structures
Fukuchi, S., Homma, K., Sakamoto, S., Nishikawa, K.
Protein fold predictions from genome sequences
database
summary
GTRD
Yevshin, Ivan;Sharipov, Ruslan;Kolmykov, Semyon;Kondrakhin, Yury;Kolpakov, Fedor
Gene Transcription Regulation Database
database
summary
GtRDB - Genomic tRNA Database
Todd M. Lowe
tRNA sequences in complete genomes
database
summary
GutMDisorder
Cheng, Liang; Qi, Changlu; Cai, Yiting; Qian, Kai; Li, Xuefeng; Ren, Jialiang; Wang, Ping; Fu, Tongze; zhao, tianyi; Zhang, Xue1
gutMDisorder v2.0: a comprehensive database for dysbiosis of the gut microb
database
summary
GutMetaNet
Shuai Cheng Li
Horizontal gene transfer and functional redundancy in the human gut microbiome
database
summary
gutMGene
Cheng, Liang; Qi, Changlu; Yang, Haixiu; Lu, Minke; Cai, Yiting; Fu, Tongze; Ren, Jialiang; Jin, Qu; Zhang, Xue1
Target genes of gut microbes and microbial metabolites in human and mouse
database
summary
gutMSNP
Liang Cheng; et al.
gutMSNP: a comprehensive database for human gut microbial single nucleotide polymorphisms
database
summary
GVM
Song, Shuhui; Li, Cuiping; Tian, Dongmei; Tang, Bi-Xia; Liu, Xiaonan; Teng, Xufei; Zhao, Wen-Ming; Zhang, Zhang
Genome Variation Map
database
summary
GWAS Atlas
Liu, Xiaonan; Tian, Dongmei; Li, Cuiping; Tang, Bi-Xia; Wang, Zhonghuang; Zhang, Rongqin; Pan, Yitong; Wang, Yi; Zou, Dong; Zhang, Zhang; Song, Shuhui
GWAS Atlas: an updated knowledgebase integrating more curated associations
database
summary
GWAS Catalog
Sollis, Elliot; Mosaku, Abayomi; Abid, Ala; Buniello, Annalisa; Cerezo, Maria; Gil, Laurent; Groza, Tudor; Gunes, Osman; Hall, Peggy; Hayhurst, James D; Ibrahim, Arwa; Ji, Yue; John, Sajo; Lewis, Elizabeth; MacArthur, Jacqueline; McMahon, Aoife; Osumi-Sut
The NHGRI-EBI GWAS Catalog: Knowledgebase and deposition resource
database
summary
GWAS Central
Beck, Tim; Rowlands, Thomas; Shorter, Tom; Brookes, Anthony
GWAS Central: an expanding resource for finding and visualising genotype an
database
summary
GWAS Diagram Browser
Parkinson, Helen; Welter, Danielle; MacArthur, Jacqueline; Morales, Joannella; Burdett, Tony; Hall, Peggy; Junkins, Heather; Klemm, Alan; Xu, Ming; Flicek, Paul; Manolio, Teri; Hindorff, Lucia
No description supplied
database
summary
GWASdb
Junwen Wang
Human genetic variants identified by genome wide association studies
database
summary
GWAShug
Sheng Yang
Diverse GWAS methods
database
summary
GWIDD
Petras J. Kundrotas, Zhengwei Zhu, and Ilya A. Vakser
Genome-WIde Docking Database: 3D structures of protein complexes
database
summary
GWIPS-viz
Baranov, Pavel; Michel, Audrey; Kiniry, Stephen; O'Connor, Patrick; Mullan, James
No description supplied
database
summary
GWIPS-viz
Michel, Audrey; Fox, Gearoid; Kiran, Anmol; De Bo, Christof; O'Connor, Patrick; Heathy, Steaphen; Mullan, James; Donohue, Claire; Higgins, Desmond; Baranov, Pavel
Genome-Wide Information on Protein Synthesis in vivo using ribosome profiling
database
summary
GyDB
Gypsy database of mobile genetic elements
database
summary
H-Invitational Database, an integrated database of human genes and transcripts
Takeda, J.
, Yamasaki, C.
, Murakami, K.
, Sera, M.1, Hara, Y.
, Nagai, Y.
, Mamiya, K.
, Endo, T.
, Habara, T.
, Obi, N.
, Imanishi, T.
and Gojobori, T.
1,2
Full-length human cDNA clones
database
summary
H2DB
Eli Kaminuma
Heritability data for various species with trait-associated genomic loci
database
summary
HACER: an atlas of human active enhancers to interpret regulatory variants
Wang, Jing;Dai, Xizhen;Berry, Lynne D;Cogan, Joy D;Liu, Qi;Shyr, Yu
No description supplied
database
summary
HAGR
de MagalhÃƒÂ£es, JoÃƒÂ£o Pedro; Tacutu, Robi; Thornton, Daniel; Budovsky, Arie; Johnson, Emily; Barardo, Diogo; Craig, Thomas; Lehmann, Gilad; Toren, Dmitri; Fraifeld, Vadim
No description supplied
database
summary
HAGR
de MagalhÃ£es, JoÃ£o Pedro; Farooq, Zoya; arantes, gabriel; Avelar, Roberto; Barardo, Diogo; Chatsirisupachai, Kasit; Clark, Peter; De Almeida Lopes, Ines; Johnson, Emily; Novoa, Guy; senez, ludovic; De-Souza, Evandro A.; Talay, Angelo; Thornton, Daniel; To, Paul
Human Ageing Genomic Resources: updates on key databases in ageing research
database
summary
HAGR - Human Ageing Genomic Resources
Tacutu, R.
, Craig, T.
, Budovsky, A.
2,3
, Wuttke, D.
, Lehmann, G.
, Taranukha, D
, Costa, J.
, Fraifeld, V.E.
and de MagalhÃƒÆ’es J.P.
1,*
Genes related to ageing in humans and model organisms
database
summary
HALL
ZHANG, WEIQI; Hao, Li; Wu, Song; Li, Jiaming; xiong, zhuang; Yang, Kuan; Ye, Weidong; REN, JIE; Wang, Qiaoran; Xiong, Muzhao; Zheng, Zikai; Zhang, Shuo; Han, Zichu; Yang, Peng; Jiang, Beier; Ping, Jiale; Zuo, Yuesheng; Lu, Yongxiao; Cheng, Zhaiqiao; Yan, Haoteng; Wang, Si; Ma, Shuai; Zhang, Bing,.; Zhang, Feng; Ye, Jinlin; qu, jing; Liu, Guang-Hui; Yang, Yun-Gui; Bao, Yi-Ming
HALL: a comprehensive database for human aging and longevity studies
database
summary
HAMAP
Bridge, Alan; Pedruzzi, Ivo; Rivoire, Catherine; Auchincloss, Andrea; Coudert, Elisabeth; Keller, Guillaume; de Castro, Edouard; Baratin, Delphine; Cuche, BÃƒÂ©atrice; Bougueleret, Lydie; Poux, Sylvain; Redaschi, Nicole; Xenarios, Ioannis
High-quality Automated and Manual Annotation of microbial Proteomes
database
summary
HaploReg
Luke Ward
SNP-centric access to chromatin state information
database
summary
HapMap Project (discontinued)
Thorisson, G.A., Stein, L.D.
SNP Consortium data
database
summary
HapScoreDB
Alessandro Romanel; et al.
HapScoreDB: the database of PLM-derived functional scores for haplotype-resolved genomic variants
database
summary
HaptenDB
Singh M.K., Srivastava S., Raghava G.P.S. and Varshney G.C
Curated database of hapten molecules
database
summary
HbVar
Patrinos, George; Giardine, Belinda; Joly, Philippe; Pissard, Serge; Wajcman, Henri; Chui, David; Hardison, Ross
Human haemoglobin variants and thalassemias
database
summary
HBVdb
Christophe Combet
A knowledge database for the Hepatitis B Virus
database
summary
HCAD - Human Chromosome Aberration Database
hoffmann@cbio.mskcc.org or valencia@cnio.es
Chromosomal breakpoints and affected genes
database
summary
HCMDB
Dong, Dong; Zheng, Guantao; Ma, Yijie; Li, Wushuang
Metastasis is the main event leading to death in cancer patients. Over the
database
summary
HCV Database
Carla Kuiken
Variation in hepatitis C virus sequences
database
summary
HDBase
Nat Goodman
A website for Huntington's disease research
database
summary
HDO
Alexander Tropsha; et al.
The DO-KB Knowledgebase 2026 Update: Expanding programmatic and landscape-scale access to the Human Disease Ontology
database
summary
HDO
Schriml, Lynn; Baron, J. Allen; Sanchez-Beato Johnson, Claudia; Schor, Michael; Olley, Dustin; Nickle, Lance; Bearer, Cynthia; Lichenstein, Richard; Koka, Rima; Felix, Victor; Munro, James; Bello, Susan; Bisordi, Katie; Greene, Carol
The DO-KB Knowledgebase: A 20-year journey developing the disease open science ecosystem
database
summary
HEDD
ZHANG, ZHENGDONG; WANG, ZHEN; ZHANG, QUANWEI; ZHANG, WEN; Lin, Jhih-rong; CAI, YING; Mitra, Joydeep
No description supplied
database
summary
HEG-DB
Predicted highly expressed genes in prokaryotic genomes
database
summary
Helminth.net
Martin, John,; Rosa, Bruce; Ozersky, Philip; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Bhonagiri-Palsikar, Veena; Tyagi, Rahul; Wang, Qi,; Choi, Young-Jun; Gao, Xin; McNulty, Samantha; Brindley, Paul; Mitreva, Makedonka
Parasitic nematode sequencing project
database
summary
HemBase
Genes transcribed in differentiating human erythroid cells
database
summary
Heme Protein Database
Heme types, protein structures, axial ligands and Em values
database
summary
Hemolytik
Raghava, Gajender; Gautam, Ankur; Chaudhary, Kumardeep; Singh, Sandeep; Joshi, Anshika; Anand, Priya; Tuknait, Abhishek; Mathur, Deepika; Varshney, Grish
A Database of Hemolytic and Non-hemolytic Peptides
database
summary
HeRA
Han, Leng; Zhang, Zhao.; Hong, Wei; Ruan, Hang; Jing, Ying; Li, Shengli; Liu, Yaoming; Wang, Jun; Li, Wenbo; Diao, Lixia
Human enhancer RNA Atlas
database
summary
HERB
Zhao, Yi; Fang, ShuangSang; Dong, Lei; Liu, Liu; Guo, Jin-Cheng; Zhao, LianHe; Zhang, JiaYuan; Bu, Dechao; Liu, XinKui; Huo, PeiPei; Cao, WanChen; Dong, QiongYe; Wu, Jia-Rui; Wu, Yang
High-throughput Experiment- and Reference-guided dataBase of TCM
database
summary
Herb Ingredient Targets
Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, and Zhiwei Cao
Herbal active Ingredients and their Targets
database
summary
HERVd - Human Endogenous Retrovirus database
Human endogenous retrovirus database
database
summary
HervD Atlas
Chen, Fei; Li, Cuidan; Qian, Qiheng; Yan, Chenghao; Lu, Mingming; Li, Lin; Li, Pan; Fan, Zhuojing; Lei, Wenyan; Shang, Kang; Wang, Peihan; Wang, Jie; Lu, Tianyi; Huang, Yuting; Yang, Hongwei; Wei, Haobin; Han, Jingwan; Xiao, Jingfa
HervD Atlas: A Curated Knowledgebase of Associations Between Human Endogenous Retroviruses and Diseases
database
summary
Het-PDB Navi
Yamaguchi, A.
, Tomoda, S.
, Yura, K.
, Go, M.
Protein-small molecule interactions
database
summary
HEXEvent
Klemens Hertel
Human Exone Splicing Events
database
summary
HFV database
Carla Kuiken
Hemorrhagic fever virus sequence database
database
summary
HGD
Elsik, Christine; Walsh, Amy; Triant, Deborah; Le Tourneau, Justin; Shamimuzzaman, Md
Hymenoptera Genome Database
database
summary
HGD
Duan, Guangya; Wu, Gangao; Chen, Xiaoning; Tian, Dongmei; Li, Zhaohua; sun, yanling; Du, Zhenglin1; Hao, Lili; Song, Shuhui; Gao, Yuan; Xiao, Jingfa; Zhang, Zhang; Bao, Yi-Ming; Tang, Bi-Xia; Zhao, Wen-Ming
Homolog Gene Database - expression, traits, variants across species
database
summary
HGNC/VGNC
Seal, Ruth; Braschi, Bryony; Gray, Kristian; Jones, Tamsin; Tweedie, Susan; Haim-Vilmovsky, Liora; Bruford, Elspeth
Genenames.org: the HGNC resources in 2023
database
summary
HGPD
Maruyama, Yukio; Kawamura, Yoshifumi; Nishikawa, Tetsuo; Isogai, Takao; Nomura, Nobuo; Goshima, Naoki
Human Gene and Protein Database: experimental results of human proteomics
database
summary
HGT-DB, Horizontal Gene Transfer-DataBase
Garcia-Vallve, S., Guzman, E, Montero, MA., Romeu, A.
Putative horizontally-transferred genes in prokaryotic genomes
database
summary
HGTree
Choi, Youngseok; Ahn, Sojin; Park, Myeongkyu; Lee, SaetByeol; Cho, Seoae; Kim, Heebal
HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method
database
summary
HGTree
Jeong, Hyeon soo; Sung, Samsun; Kwon, Taehyung; Seo, Minseok; Caetano-Anolles, Kelsey; Choi, Sang Ho; Cho, Seoae; Nasir, Arshan; Kim, Heebal
A database of horizontally transferred genes
database
summary
HGVS Databases
A compilation of human mutation databases
database
summary
HHCDB
Zhang, Yan; Wang, Hongli; Su, Mu; Xing, Jie; Zhou, Jie; Wang, Jinzhang; Chen, Long; Dong, Haomin; Xue, Wenhui; Liu, Yubo; Wu, Qiong
HHCDB: A Database of Human Heterochromatin Regions
database
summary
HHMD
Yan Zhang, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, and Xia Li
Human Histone Modification Database
database
summary
HIC-Up
Kleywegt, G.J.
Structures of small molecules (³hetero-compounds²)
database
summary
HiChIPdb
Wong, Wing; Zeng, Wanwen; Liu, Qiao; Yin, Qijin; Jiang, Rui
HiChIP regulatory interactions
database
summary
HieranoiDB
Kaduk, Mateusz; Riegler, Christian; Lemp, Oliver; Sonnhammer, Erik
Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2
database
summary
HIPPIE
Schaefer, Martin; Alanis-Lobato, Gregorio; Andrade, Miguel
Human Integrated Protein-Protein Interaction rEference
database
summary
HipSci
Clarke, Laura; Streeter, Ian; Harrison, Peter; Faulconbridge, Adam; Flicek, Paul; Parkinson, Helen
Human Induced Pluripotent Stem Cells Initiative
database
summary
Histome
Khare SP
1,2
, Habib F
, Sharma R
, Gadewal N
, Gupta S
, Galande S
Human histone database
database
summary
HIT
Cao, Zhiwei; Yan, Deyu; Zheng, Genhui; Wang, Caicui; Chen, Zikun; mao, tiantian; Gao, Jian; Yan, Yu; Chen, Xiangyi; Ji, XueJie; Yu, Jinyu; Mo, Saifeng; Wen, Haonan; Han, Wenhao; Zhou, MengDi; Wang, Yuan; Wang, Jun; Tang, KaiLin,
HIT 2.0: An enhanced platform for Herbal Ingredients' Targets
database
summary
HitPredict
Hao Ye
1,2
, Li Ye
1,2
, Hong Kang
, Duanfeng Zhang
, Lin Tao
4,5
, Kailin Tang
Xueping Liu
1,2
, Ruixin Zhu
, Qi Liu
, Y. Z. Chen
, Yixue Li
2,6
, and Zhiwei Cao
Quality assessed protein-protein interactions in 9 species
database
summary
Hits
Pagni, M.
, Falquet, L.
, Iseli, C.
, Jongeneel, V.
, Junier, T.
, Bucher, P.
A database of protein domains and motifs
database
summary
HIV Drug Resistance Database
Urvi Parikh, Brendan A. Larder, John W. Mellors, Raymond F Schinazi, Charles E. Calef
Mutations in HIV genes that confer resistance to anti-HIV drugs
database
summary
HIV RT and Protease Sequence Database
Rhee, S.-Y., Gonzales, M.J., Kantor, R., Betts, B.J., Ravela, J., Shafer, R.W.
HIV reverse transcriptase and protease sequences
database
summary
HIV-1
Pruitt, Kim; Ako-Adjei, Danso; Fu, William; Wallin, Craig; Katz, Kenneth; Song, Guangfeng; Darji, Dakshesh; Brister, J.; Ptak, Roger
Interactions between HIV-1 and human proteins
database
summary
HLRMDB
Lianbo Pan; et al.
HLRMDB: a comprehensive database of the human microbiome with metagenomic linkages
database
summary
HLungDB
Lishan Wang, Yuanyuan Xiong, Yihua Sun, Zhaoyuan Fang, Li Li, Hongbin Ji, and Tieliu Shi
Database of Human Lung Cancer Research
database
summary
HMDB
Wishart, David; Guo, An Chi; Oler, Eponine; Wang, Fei; Anjum, Afia; Peters, Harrison; Dizon, Raynard; Sayeeda, Zinat; Tian, Siyang; Lee, Brian; Berjanskii, Mark; Mah, Robert; Yamamoto, Mai; Jovel, Juan; Torres-Calzada, Claudia; Hiebert-Giesbrecht, Mickel;
HMDB 5.0: The Human Metabolome Database for 2022
database
summary
HMDB
Wishart, David; Djoumbou, Yannick; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vazquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Liang, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Jack; Badran, Hasan; Grant, Jason; Serra Cayuela, Arnau; Liu, Yifeng; Mandal, Rupasri; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael.; Manach, Claudine; Scalbert, Augustin
No description supplied
database
summary
HMDB - The Human Metabolome Database
Wishart D.S.
1,5,7
, Tzur D.
, Knox C.
, Eisner R.
, Guo A.C.
, Young N.
, Cheng D.
, Jewell K.
, Arndt D.
, Sawhney S.
, Fung C.
, Nikolai L.
, Lewis M.
, Coutouly M.-A.
, Forsythe I.
, Tang P.
, Shrivastava S.
, Jeroncic K.
, Stothard P.
, Amegbey G.
, Block D.
, Hau D.D.
, Wagner J.
, Miniaci J.
, Clements M.
, Gebremedhin M.
, Guo N.
, Zhang Y.
, Duggan G.E.
, MacInnis G.D.
, Weljie A.M.
, Dowlatabadi R.
, Bamforth F.
, Clive D.
, Greiner R.
, Li L.
, Marrie M.
, Sykes B.D.
, Vogel H.J.
, Querengesser L.
Curated human metabolite and metabolism data
database
summary
HMDD
Cui, Chunmei; Zhong, Bitao; Fan, Rui; Cui, Qinghua
HMDD v4.0: a database for experimentally supported human microRNA-disease associations
database
summary
HMDD v2.0 - Human microRNA Disease Database version 2.0
ng Li
1,2
, Chengxiang Qiu
, Jian Tu
2,4
, Bin Geng
, Jichun Yang
, Tianzi Jiang
and Qinghua Cui
2,4
Human MicroRNA and Disease Associations
database
summary
HMPD
Human mitochondrial protein database
database
summary
HmtDB - Human Mitochondrial DataBase
Rubino, Francesco; Piredda, Roberta; Calabrese, Francesco; Simone, Domenico; Lang, Martin; Calabrese, Claudia; Petruzzella, Vittoria; Tommaseo-Ponzetta, Mila; Gasparre, Giuseppe; Attimonelli, Marcella
Variability data and tools for analysis of human mitochondrial genome sequences
database
summary
HOCOMOCO
Kulakovskiy, Ivan; Vorontsov, Ilya; Eliseeva, Irina; Zinkevich, Arsenii; Nikonov, Michael; Abramov, Sergey; Boytsov, Alexandr; Kamenets, Vasily; Kasianova, Alexandra; Kolmykov, Semyon; Yevshin, Ivan; Favorov, Alexander.; Medvedeva, Yulia; Jolma, Arttu; Ko
HOCOMOCO of 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
database
summary
HOCOMOCO
Kulakovskiy, Ivan; Vorontsov, Ilya; Yevshin, Ivan; Sharipov, Ruslan; Fedorova, Alla; Rumynskiy, Evgeniy; Medvedeva, Yulia; Mora, Arturo; Bajic, Vladimir; Papatsenko, Dmitry; Kolpakov, Fedor; Makeev, Vsevolod
HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v11 provides transcr
database
summary
HOCOMOCO
Ivan Kulakovskiy
HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor binding site models
database
summary
HOINVGEN
Ingo Paulsen
and Arndt von Haeseler
2,3,4,5
Homologous genes in invertebrate genomes
database
summary
Hollywood
Exon annotation database
database
summary
HomoloGene
Automatically detected homologous genes in complete eukaryotic genomes
database
summary
HOMSTRAD - Homologous Structure Alignment Database
Curated structure-based alignments for protein families
database
summary
HoPaCI-DB
Ruepp, Andreas; Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias; Frangoulidis, Dimitrios; KastenmÃƒÂ¼ller, Gabi; Voulhoux, RomÃƒÂ©
The Host-Pathogen Interaction Database of Pseudomonas aeruginosa and Coxiella spp.
database
summary
Hoppsigen
Human and mouse homologous processed pseudogenes
database
summary
HORDE - Human Olfactory Receptor Data Exploratorium
Olender, T., Glusman, G., Feldmesser, E., Khen, M., Lancet, D.
Olfactory receptor genes and proteins
database
summary
HotPoint
Hot spots (functionally and structurally important residues) in protein interfaces
database
summary
HotRegion
Ozlem Keskin
Database of interaction Hotspots
database
summary
Housekeeping Transcript Atlas
Hounkpe, Bidossessi; Chenou, Francine; de Lima, Franciele; de Paula, Erich
Human and mouse housekeeping genes
database
summary
HOWDY
Koike, T., Tsurumine, M., Inoue, A., Uchida, N., Iwashima, M., Suzuki, K., Kuroda, M.
Integrated human genomic information
database
summary
HOX-PRO
Clustering of homeobox genes
database
summary
hp-DPI
Database of protein interactions in
Helicobacter pylori
database
summary
HPID - Human Protein Interaction database
Human protein interaction database
database
summary
HPMCD
Lawley, Trevor; Forster, Samuel; Browne, Hilary; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert
Human Pan-Microbial Communities Database
database
summary
HPMR - Human Plasma Membrane Receptome
Plasma membrane protein sequences, literature, and expression database
database
summary
HPRD - Human Protein Reference Database
Domain architecture, post-translational modifications, interaction networks and disease
database
summary
HProteome-BSite
Sim, Jiho; Kwon, Sohee; Seok, Chaok
Predicted binding sites and ligands in the human 3D proteome
database
summary
hPSCreg
Kurtz, Andreas; Seltmann, Stefanie; Lekschas, Fritz; MÃƒÂ¼ller, Robert; Stachelscheid, Harald; Bittner, Marie-Sophie; Zhang, Weiping; Kidane, Luam; Seriola, Anna; Veiga, Anna; Stacey, Glyn
Human Pluripotent Stem Cell registry
database
summary
HPTAA
Human potential tumor-associated antigens
database
summary
HRaP - Database of occurrence of HomoRepeats and Patterns in proteomes
Lobanov, M.Yu., Sokolovskiy, I.V. and Galzitskaya, O.V.
HomoRepeats and Patterns
database
summary
HSCGD
Fu, Jiye; He, Shiyang; Yang, Yixuan; Chen, Zitong; Qiao, Yi; Lu, Na; Lu, Zuhong; Tu, Jing
Human single-cell genomes
database
summary
HTCA
Li, Xuexin; Pan, Lu; Li, Weiyuan; Liao, Zehuan; Zhang, Xiaolu
Single cell transcriptomes and analytical tools
database
summary
HTPSELEX
Transcription factor binding site sequences obtained using high-throughput SELEX method
database
summary
huARdb
LLize Wu, Ziwei Xue, Siqian Jin, Jinchun Zhang, Yixin Guo, Yadan Bai, Xuexiao Jin, Chaochen Wang, Lie Wang, Zuozhu Liu, James Q. Wang, Linrong Lu and Wanlu Liu
Human Antigen Receptor Consortium [CHECK]
database
summary
Human Disease Ontology
Schriml, Lynn; Munro, James; Schor, Mike; Olley, Dustin; McCracken, Carrie; Felix, Victor; Baron, Allen; Jackson, Rebecca; Bello, Susan; Bearer, Cynthia; Lichenstein, Richard; Bisordi, Katie; Campion, Nicole; Giglio, Michelle; Greene, Carol
The Human Disease Ontology 2022 update
database
summary
Human MtDB
Ingman M.
Human mitochondrial genome database
database
summary
Human OligoGenome Resource
Daniel Newburger
Oligonucleotides for targeted resequencing of the human genome
database
summary
Human Phenotype Ontology
Robinson, Peter; Gargano, Michael; Matentzoglu, Nicolas; Coleman, Ben; Toro, Sabrina; Carmody, Leigh; Harris, Nomi; Munoz-Torres, Monica; Danis, Daniel; Mungall, Christopher; Koehler, Sebastian; Haendel, Melissa
Standardized vocabulary of phenotypic abnormalities in human disease
database
summary
Human Proteinpedia
Community portal for sharing and integration of human proteomic data
database
summary
Human Proteoform Atlas
Kelleher, Neil; Hollas, Michael; Robey, Matthew; Fellers, Ryan; LeDuc, Richard; Thomas, Paul
Human proteoforms
database
summary
Human-scATAC-Corpus
Jiang, Rui; Wang, Xiaoxiao; Zhang, Xinyi; Zhang, Wei; et al.
Human-scATAC-Corpus: a comprehensive database of scATAC-seq data
database
summary
HumanMetagenomeDB
Nunes da Rocha, Ulisses; Kasmanas, Jonas; BartholomÃƒÂ¤us, Alexander; CorrÃƒÂªa, Felipe; Tal, Tamara; Jehmlich, Nico; Herberth, Gunda; von Bergen, Martin; Stadler, Peter F.; Carvalho, AndrÃƒÂ© C P L F
Curated and standardized metadata for human metagenomes
database
summary
HumanNet
Lee, Insuk; Kim, Chan Yeong; Cha, Junha; Yang, Sunmo; Kim, Eiru; Marcotte, Edward; Hart, Traver
HumanNet v3: An improved human functional gene network for disease research
database
summary
HUSCH
Shi, Xiaoying; Yu, Zhiguang; Ren, Pengfei; Ding, Xuanxin; Song, Jiaming; Zhang, Jing; Li, Taiwen; Wang, Chenfei
Human Universal Single Cell Hub
database
summary
Hymenoptera Genome
Monica C. Munoz-Torres, Justin T. Reese, Christopher P. Childers, Anna K. Bennett, Jaideep P. Sundaram, Kevin L. Childs, Juan M. Anzola, Natalia Milshina, and Christine G. Elsik
Genome sequences and annotation for honey bee Apis mellifera and the parasitoid wasp, Nasonia vitripennis
database
summary
HyperCLDB
Romano P, Manniello MA, Aresu O, Armento M, Cesaro M, Parodi B.
Hypertext version of the Cell Line Data Base
database
summary
I2D - Interologous Interaction Database
Brown K.R.
1,2
and Jurisica I.
1,2,3
Online Predicted Human Interaction Database
database
summary
i5k Workspace@NAL
Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin
Arthropod genome projects
database
summary
IAnimal
Fu, Yuhua; Liu, Hong; Dou, Jingwen; Wang, Yue; Liao, Yong; Huang, Xin; Tang, Zhenshuang; Xu, Jingya; Yin, Dong; Zhu, Shilin; Liu, Yangfan; Shen, Xiong; Liu, Hengyi; Liu, Jiaqi; Yang, Xin; Zhang, Yi; Xiang, Yue; Li, Jingjin; Zheng, Zhuqing; Zhao, Yunxia; M
Mulit-omics data for 21 animals
database
summary
IARC TP53 Database
Olivier, M.
, Hollstein, M.
, Harris, C.C..
, and Hainaut, P.
Human TP53 somatic and germline mutations
database
summary
iBeetle-Base
Doenitz, Juergen; Gerischer, Lizzy; Hahnke, Stefan; Pfeiffer, Stefan; Bucher, Gregor
No description supplied
database
summary
iBeetle-Base
Doenitz, Juergen; Schmitt-Engel, Christian; Grossmann, Daniela; Gerischer, Lizzy; Tech, Maike; Schoppmeier, Michael; Klinger, Martin; Bucher, Gregor
Phenotypes of a large scale RNAi screen in the red flour beetle Tribolium castaneum
database
summary
IBIS
Panchenko, Anna; Shoemaker, Benjamin; Zhang, Dachuan; Tyagi, Manoj; Thangudu, Ratna; Fong, Jessica; Marchler-Bauer, Aron; Bryant, Steve; Madej, Tom
Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites
database
summary
IC4R
Zhang, Zhang; Hao, Lili; Xia, Lin; Huang, Dawei; Yang, Li; Xu, Xingjian; Yan, Wei; Zhang, Ye; Zou, Dong; Liu, Siqi; Sang, Jian; Deng, Wankun; Wang, Yongbo; Cheng, Han; Ma, Lina; Yuan, Fangfang; Zhong, Jun; Li, Qian; Wu, Shuangyang; He, Zilong; Luo, Yingfeng; Wang, Xin; Ji, Zhaohua; Wang, Xiangfeng; Xue, Yu; Chen, Ling-ling .; Xiao, Jingfa; Zhao, Wen-Ming; Chen, Fei; Zhang, Huiyong; He, Hang; Hu, Songnian
Information Commons for Rice
database
summary
ICEberg
Hong-Yu OU
Integrative and Conjugative Elements in Bacteria
database
summary
ICEBERG
OU, Hong-Yu; Wang, Meng; Liu, Guitian; Liu, Meng; Tai, Cui; Deng, Zixin1; Song, Jiangning
ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria
database
summary
ICG
Hao, Lili; Sang, Jian; Wang, Zhennan; Li, Man'; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wen-Ming; Bao, Yi-Ming; Xiao, Jingfa; Hu, Songnian; Zhang, Zhang
No description supplied
database
summary
iCSDB
Lee, Sanghyuk; Choi, Ahyoung; Jang, Insu; Han, Heewon; Kim, Min-Seo; Choi, Jinhyuk; Lee, Jieun; Cho, Sung-Yup; Jun, Yukyung; Lee, Charles; Kim, Jaesang; Lee, Byungwook
integrated CRISPR Screens DataBase
database
summary
IDDB
Zhang, Jian; Wu, Jing; Li, Danjun; He, Xinheng; Liu, Xinyi.; Li, Qian '; Li, Xinyi; Wei, Jiale; Li, Mingyu; Rehman, Ashfaq Ur; Wu, Chengwei; Xia, Yujia; Lu, Xuefeng
Infertility Disease DataBase
database
summary
IDEAL
Fukuchi, Satoshi; Amemiya, Takayuki; Sakamoto, Shigetaka; Nobe, Yukiko; Hosoda, Kazuo; Kado, Yumiko; Murakami, Seiko; Koike, Ryotaro; Hiroaki, Hidekazu; Ota, Motonori
Intrinsically Disordered proteins with Extensive Annotations and Literature
database
summary
IEAtlas
Xu, Juan; Cai, Yangyang; Lv, Dezhong; Li, Donghao; Yin, Jiaqi; Ma, Yingying; Luo, Ya; Fu, Limei; Ding, Na; Li, Yongsheng; Pan, Zhenwei; Li, Xia
HLA-presented immune epitopes from non-coding regions etc
database
summary
IEDB
Vita, Randi; Overton, James; Greenbaum, Jason; Ponomarenko, Julia; Clark, Jason; Cantrell, Jason; Wheeler, Daniel; Gabbard, Joseph; Hix, Deborah; Sette, Alessandro; Peters, Bjoern
Immune Epitope Database: Experimentally characterized B- and T-cell immune response targets
database
summary
IEDB-3D
Julia Ponomarenko
1,2
, Nikitas Papangelopoulos
, Dirk M. Zajonc
, Bjoern Peters
,Alessandro Sette
and Philip E. Bourne
1,2
Structural data within the Immune Epitope Database
database
summary
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains
Guo, Yaping;Peng, Di;Zhou, Jiaqi;Lin, Shaofeng;Wang, Chenwei;Ning, Wanshan;Xu, Haodong;Deng, Wankun;Xue, Yu
No description supplied
database
summary
iFish
Jing Gong; et al.
iFish: a comprehensive multi-omics database for fish genetics
database
summary
IGDB.NSCLC
Yuh-Shan Jou
Integrated Genomic Database of Non-Small Cell Lung Cancer
database
summary
IGDD
Sanchari Pradhan, Mainak Sengupta, Anirban Dutta, Kausik Bhattacharyya, Sumit K. Bag, Chitra Dutta, and Kunal Ray
Indian Genetic Disease Database
database
summary
iGNM
Yang, Lee-Wei; Li, Hongchun; Chang, Yuan-Yu; Bahar, Ivet
Protein functional motions based on Gaussian Network Model
database
summary
IGRhCellID
Cheng-Kai Shiau, De-Leung Gu, Chian-Feng Chen, Chi-Hung Lin, and Yuh-Shan Jou
Human Cell Lines Identification Resources
database
summary
IGSR
Flicek, Paul; Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily,; Lowy, Ernesto; TassÃƒÂ©, Anne-Marie
International Genome Sample Resource
database
summary
IGVF Catalog
Ling Wang; et al.
IGVF Catalog: a comprehensive database of functional genomic variants
database
summary
IID
Jurisica, Igor; Kotlyar, Max; Pastrello, Chiara; Ahmed, Zuhaib; Chee, Justin; Varyova, Zofia
IID 2021: towards context-specific protein interaction analyses by increase
database
summary
IKMC
Martin Ringwald
, Vivek Iyer
, Jeremy C. Mason
, Kevin R. Stone
, Hamsa D. Tadepally
, James A. Kadin
, Carol J. Bult
, Janan T. Eppig
, Darren J. Oakley
, Sebastien Briois
, Elia Stupka
, Vincenza Maselli
, Damian Smedley
, Songyan Liu
,Jens Hansen
, Richard Baldock
, Geoff G. Hicks
and William C. Skarnes
Data and resources from the International Knockout Mouse Consortium
database
summary
IL2Rgbase [Retired]
X-linked severe combined immunodeficiency mutations
database
summary
IMG Genomes
Roux, Simon; PÃƒÂ¡ez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Reddy, T.B.K.; Nayfach, Stephen; Schulz, Frederik; Call, Lee; Neches, Russell Y; Woyke, Tanja; Ivanova, Natalia N; Eloe-Fadrosh, Emiley A; Kyrpides Nikos C
Comparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute
database
summary
IMG-ABC
Hadjithomas, Michalis; Chen, I-Min; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Szeto, Ernest; Markowitz, Victor; Kyrpides, Nikos; Ivanova, Natalia
Atlas of Biosynthetic gene Clusters for secondary metabolites
database
summary
IMG/M
Chen, I-Min; Chu, Ken; Palaniappan, Krishna; Ratner, Anna; Huang, Jinghua; Huntemann, Marcel; Hajek, Patrick; Ritter, Stephan; Webb, Cody; Wu, Dongying; Varghese, Neha; Reddy, TBK; Mukherjee, Supratim; Ovchinnikova, Galina; Nolan, Matt; Seshadri, Rekha; R
The IMG/M data management and analysis system v.7: content updates and new
database
summary
IMG/M
Chen, I-Min; Chu, Ken; Palaniappan, Krishna; Ratner, Anna; Huang, Jinghua; Huntemann, Marcel; Hajek, Patrick; Ritter, Stephan; Varghese, Neha; Seshadri, Rekha; Roux, Simon; Woyke, Tanja; Eloe-Fadrosh, Emiley; Ivanova, Natalia; Kyrpides, Nikos
A data management and analysis system for metagenomes
database
summary
IMG/PR
Camargo, Antonio; Call, Lee; Roux, Simon; Nayfach, Stephen; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Chen, I-Min; Baltrus, David; CastaÃ±eda-Barba, Salvador; de la Cruz, Fernando; Funnell, Barbara; Hall, James; Mukhopadhyay, Aindrila; Rocha, Eduardo;
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
database
summary
IMG/VR
Camargo, Antonio; Nayfach, Stephen; Chen, I-Min; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Ritter, Stephan; Reddy, TBK; Mukherjee, Supratim; Schulz, Frederik; Call, Lee; Neches, Russell; Woyke, Tanja; Ivanova, Natalia; Eloe-Fadrosh, Emiley; Kyrpides,
IMG/VR v4: an expanded database of uncultivated virus genomes within a fram
database
summary
IMG/VR v3
Roux, Simon; Paez-Espino, David; Chen, I-Min; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Reddy, TBK; Nayfach, Stephen; Schulz, Frederik; Call, Lee; Neches, Russell; Ivanova, Natalia; Eloe-Fadrosh, Emiley; Kyrpides, Nikos
Comparative analysis of viral genomes at the DOE Joint Genome Institute
database
summary
IMGT/3Dstructure-DB
Ehrenman, F., Kaas, Q., and Lefranc, M.-P.
Immunoglobulin, T cell receptor, MHC and RPI 3D structures from human and other vertebrate species
database
summary
IMGT/GENE-DB
Giudicelli, V., Duroux, P., Ginestoux, C., Bellahcene, F., and Lefranc, M.-P.
Immunoglobulin and T cell receptor genes from human and other vertebrate species
database
summary
IMGT/LIGM-DB
Duroux, P., Giudicelli, V., Jabado-Michaloud, J., Regnier, L., Lefranc, M.-P.
Immunoglobulin and T cell receptor sequences from human and other vertebrate species
database
summary
IMGT/mAb-DB
Lefranc, Marie-Paule (proxy) (contact); Giudicelli, VÃƒÂ©ronique; Duroux, Patrice; Michaloud, Joumana; Folch, GÃƒÂ©raldine; Aouinti, Safa; Carillon, Emilie; Duvergey, Hugo; Houles, AmÃƒÂ©lie; Paysan-Lafosse, Typhaine; Saljoqi, Saida; Sasorith, Souphatta; Lefranc, GÃƒÂ©rard; Kossida, Sofia
Database for therapeutic monoclonal antibodies
database
summary
IMGT/PRIMER-DB
Folch, G., Ehrenman, F. and Lefranc, M.-P.
Immunoglobulin and T cell receptor oligonucleotide sequences from human and other vertebrate species
database
summary
IMGTÂ® databases
Kossida, Sofia; Manso, Taciana; Folch, GÃ©raldine; Giudicelli, VÃ©ronique; Michaloud, Joumana; Duroux, Patrice; Kushwaha, Anjana; NGUEFACK NGOUNE, Viviane; Georga, Maria; Papadaki, Ariadni; Debbagh, Chahrazed; Pegorier, Perrine; Bertignac, Morgane; Hadi-Sal
IMGTÂ® databases, related tools and web resources through three main axes o
database
summary
ImmCluster
Li, Yongsheng; Jiang, Tiantongfei; Zhou, Weiwei; Sheng, Qi; Yu, Jiaxin; Xie, Yunjin; Ding, Na; zhang, Yunpeng`; Xu, Juan
Immunology cell types in normal and cancer tissues
database
summary
ImmPort
ImmPort is funded by the NIH, NIAID and DAIT in support of the NIH mission
database
summary
ImmuCo
Wang, Pingzhang; Qi, Huiying; Song, Shibin; Li, Shuang; Huang, Ningyu; Han, Wenling; Ma, Dalong
Gene coexpression in immune cells
database
summary
ImmuNet
Dmitriy Gorenshteyn, Elena Zaslavsky, Miguel Fribourg, Christopher Y. Park, Aaron K. Wong, Alicja Tadych, Boris M. Hartmann, Randy A. Albrecht, Adolfo GarcÃƒÂa-Sastre, Steven H. Kleinstein, Olga G. Troyanskaya, Stuart C. Sealfon
Many functionally important interactions between genes and proteins involve
database
summary
ImmunoBase
A community resource for type 1 diabetes research
database
summary
Immunosenescence Inventory
Weiqi Zhang
Multi-omics of immune aging
database
summary
iModulonDB
Palsson, Bernhard; Rychel, Kevin; Decker, Katherine; Sastry, Anand; Phaneuf, Patrick; Poudel, Saugat
"iModulons", groups of independently-modulated genes
database
summary
IMOTA
Keller, Andreas; Palmieri, Valeria; Backes, Christina; Ludwig, Nicole; Fehlmann, Tobias; Kern, Fabian; Meese, Eckart
Web repositories for almost all Ã¢â‚¬ËœomicsÃ¢â‚¬â„¢ types have been genera
database
summary
IMOTdb
Pugalenthi G., Bhaduri A. and Sowdhamini R.
Spatially interacting motifs in proteins
database
summary
IMP
Chen, Tong (proxy) (contact); Yang, Mei; Cui, Guanghong; Tang, Jinfu; Shen, Ye; Liu, Juan; Yuan, Yuan.'; Guo, Juan; Huang, Lu-Qi
IMP: Bridging the Gap for Medicinal Plant Genomics
database
summary
IMPC
Groza, Tudor; Lopez Gomez, Federico; Haseli Mashhadi, Hamed; MuÃ±oz-Fuentes, Violeta; Gunes, Osman; Wilson, Robert; Cacheiro, Pilar; Frost, Anthony; Keskivali-Bond, Piia; Vardal, Bora; McCoy, Aaron; Cheng, Tsz Kwan; Santos, Luis; Wells, Sara; Smedley, Dami
The International Mouse Phenotyping Consortium: Comprehensive knockout phen
database
summary
IMPC
Koscielny, Gautier; Yaikhom, Gagarine; Iyer, Vivek; Meehan, Terrence; Morgan, Hugh; Atienza-Herrero, Julian; Blake, Andrew; Chen, Chao-Kung; Easty, Richard; Di Fenza, Armida; Fiegel, Tanja; Grifiths, Mark; Horne, Alan; Karp, Natasha; Kurbatova, Natalja; Mason, Jeremy; Matthews, Peter; Oakley, Darren; Qazi, Asfand; Regnart, Jack; Retha, Ahmad; Santos, Luis; Sneddon, Duncan; Warren, Jonathan; Westerberg, Henrik; Wilson, Robert; Melvin, David; Smedley, Damian; Brown, Steve; Flicek, Paul; Skarnes, Bill; Mallon, Ann-Marie; Parkinson, Helen
International Mouse Phenotyping Consortium: an encyclopaedia of mammalian gene function
database
summary
Imprinted Gene Catalogue
Morison, I.M.
, Glaser, R.
Imprinted genes and parent-of-origin effects database
database
summary
iNClusive
Ã–ztÃ¼rk, Mehmet Ali; Icking, Leon-Samuel; Riedlberger, Andreas Martin; Widder, Jonas; Frederiksen, Anne; Stockert, Fabian; SpÃ¤dt, Michael; Edel, Nikita; Krause, Fabian; Franchini, Selene; Gerstenecker, Johanna; Ranniger, Jeremy; Gescher, Pia; Kaas, Paulina; Salavei, Pavel; Gensch, Nicole; Di Ventura, Barbara; Voigt, Karsten
iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins
database
summary
INDI
Krawczyk, Konrad; Deszynski, Piotr; Mlokosiewicz, Jakub; Volanakis, Adam; Jaszczyszyn, Igor; Castellana, Natalie; Bonissone, Stefano; Ganesan, Rajkumar
Integrated Nanobody Database for Immunoinformatics
database
summary
IndiGenomes
Scaria, Vinod; Jain, Abhinav; Bhoyar, Rahul; Pandhare, Kavita; Mishra, Anushree; Sharma, Disha; Imran, Mohamed; Senthilvel, Vigneshwar; Divakar, Mohit Kumar; Rophina, Mercy; Jolly, Bani; Batra, Arushi; Sharma, Sumit; Siwach, Sanjay; Jadhao, Arun; Palande,
Genetic variation in 1000 Indian individuals
database
summary
INFEVERS
Hereditary inflammatory disorder and familial mediterranean fever mutation data
database
summary
Influenza Research Database
Scheuermann, Richard; Zhang, Yun; Aevermann, Brian; Anderson, Tavis; Burke, David; Dauphin, Gwenaelle; Gu, Zhiping; He, Sherry; Kumar, Sanjeev; Larsen, Christopher; Lee, Alexandra; Li, Xiaomei; Macken, Catherine; Mahaffey, Colin; Pickett, Brett; Reardon, Brian; Smith, Thomas; Stewart, Lucy; Suloway, Christian; Sun, Guangyu; Tong, Lei; Vincent, Amy; Walters, Bryan; Zaremba, Sam; Zhao, Hongtao; Zhou, Liwei; Zmasek, Christian; Klem, Edward
Influenza Research Database
database
summary
INFRAFRONTIER
Meehan, Terrence; Blake, Andrew; Bottomley, Joanne; Chen, Chao-Kung; Castro, Ana; Fessele, Sabine; Fray, Martin; Kenyon, Janet; Koscielny, Gautier; Mallon, Ann-Marie; Massimi, Marzia; Matteoni, Raffaele; Relac, Mike; Steinkamp, Ralph; Wilkinson, Phil; Hrabe de Angelis, Martin; Brown, Steve; Tocchini-Valentini, Glauco; Herault, Yann; Ramirez-Solis, Ramiro; Kollias, George; Ulfhake, Brun; Demengeot, Jocelyne; Fremond, Cecile; Bosch, Fatima; Montoliu, Lluis; Soininen, Raija; Flicek, Paul; Schughart, Klaus; Brakebusch, Cord; Sedlacek, Radislav; RÃƒÂ¼licke, Thomas; McKerlie, Colin; Malissen, Bernard; Iraqi, Fuad; Jonkers, Jos; Russig, Holger; Huylebroeck, Danny; Parkinson, Helen; Raess, Michael; Hagn, Michael
European Research Infrastructure for phenotyping and archiving of model mammalian genomes
database
summary
InnateDB
Karin Breuer
A database of mammalian innate immune response
database
summary
Inparanoid
Sonnhammer, Erik L.L. (proxy); Ãƒâ€“stlund, Gabriel
A database of eukaryotic orthologs
database
summary
InSatDb
Archak S., Meduri E., Sravana Kumar P. and Nagaraju J.
Sequences and properties of insect microsatellites
database
summary
INSDC
Ilene Karsch-Mizrachi
International Nucleotide Sequence Database collaboration
database
summary
InsectBase
Li, Fei; Mei, Yang; Jing, Dong; Tang, Shenyang; Chen, Xi; Chen, Hao; Duanmu, Haonan; Cong, Yuyang; Chen, Mengyao; Ye, Xinhai; Zhou, Hang; He, Kang
InsectBase 2.0: a comprehensive gene resource for insects
database
summary
InsectBase
Li, Fei; Yin, Chuanlin; Shen, Genyu; Guo, Dianhao; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan'.; Liu, Y ing; Zhang, Yiqun; Huang, Shuiqing
Insect genomes and transcriptomes
database
summary
IntAct Molecular Interaction Database
Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal,
Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa
Ratan, Gautam Shirodkar, Odilia Lu, BÃ¡lint MÃ©szÃ¡ros, Xavier Watkins,
Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria
Jesus Martin, Simona Panni, Margaret Duesbury, Sylvain D. Vallet, Juri
Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski,
Sandra Orchard, Pablo Porras, Kalpana Panneerselvam and Henning Hermjakob
Protein-protein interaction data
database
summary
INTEDE
Jiayi Yin, Fengcheng Li, Ying Zhou, Minjie Mou, Yinjing Lu, Kangli Chen, Jia Xue, Yongchao Luo, Jianbo Fu, Xu He, Jianqing Gao, Su Zeng, Lushan Yu, Feng Zhu
Interactome of Drug-Metabolizing Enzymes
database
summary
INTEDE
Zhu, Feng; Zhang, Yang; Liu, Xingang; Li, Fengcheng; Yin, Jiayi; Yang, Hao; Li, Xuedong; Liu, Xinyu; Xu, Chai; Niu, Tianle; Zeng, Su; Jia, Qingzhong
INTEDE 2.0: the metabolic roadmap of drugs
database
summary
Integr8 (formerly Proteome Analysis Database)
Kersey P.J., Bower L., Horne A.D. and Apweiler R.
Functional classification of proteins in whole genomes
database
summary
IntEnz
AlcÃƒÆ’Ã‚Â¡ntara R.
, Ast V.
, Axelsen K.B.
, Darsow M.
, de Matos P.
, Ennis M.
, Morgat A.
2,3
and Degtyarenko K.
Integrated enzyme database and enzyme nomenclature
database
summary
Inter-Chain Beta-Sheets
Protein-protein interactions mediated by interchain beta-sheet formation
database
summary
InterActive Fly
Drosophila
genes and their roles in development
database
summary
InterDom
Putative protein domain interactions
database
summary
InterEvol
Raphael Guerois
Evolution of protein-protein Interfaces
database
summary
Interferome
Rusinova, Irina; Yu, Simon; Forster, Sam; Kannan, Anitha; Masse, Marion; Cumming, Helen; Chapman, Ross; Hertzog, Paul
Database of Interferon Regulated Genes
database
summary
InterFil
Human Intermediate Filament database
database
summary
International Gene Trap Consortium Database
International mouse Gene Trap Consortium data
database
summary
International Mouse Phenotyping Consortium Database
The International Mouse Phenotyping Consortium
data and procedures for large-scale phenotyping of knockout mouse lines
database
summary
InterPro
Bateman, Alex; Blum, Matthias; Chang, Hsin-Yu; Chuguransky, Sara; Grego, Tiago; Kandasaamy, Swaathi; Mitchell, Alex; Nuka, Gift; Paysan-Lafosse, Typhaine; Qureshi, Matloob; Raj, Shriya; Richardson, Lorna; Salazar, Gustavo; Williams, Lowri; Bork, Peer; Bridge, Alan J; Gough, Julian.; Haft, Daniel; Letunic, Ivica; Marchler-Bauer, Aron; Mi, Huaiyu'; Natale, Darren; Necci, Marco; Orengo, Christine; Pandurangan, Arun Prasad; Rivoire, Catherine; Sigrist, Christian; Sillitoe, Ian; Thanki, Narmada; Thomas, Paul; Tosatto, Silvio; Wu, Cathy; Finn, Robert
Integrated resource of protein families, domains and functional sites
database
summary
InterPro
Paysan-Lafosse, Typhaine; Blum, Matthias; Chuguransky, Sara; Grego, Tiago; LÃ¡zaro Pinto, Beatriz; Salazar, Gustavo; Bileschi, Maxwell L.; Bork, Peer; Bridge, Alan J; Colwell, Lucy; Gough, Julian.; Haft, Daniel; LetuniÄ‡, Ivica; Marchler-Bauer, Aron; Mi, Hu
InterPro in 2022
database
summary
InterRNA
Firdaus Raih, Mohd; Appasamy, Sri; Yusof Hamdani, Hazrina; Ramlan, Effirul
Base interactions in RNA structures
database
summary
intOGen
The Biomedical Genomics Group
Integrative Onco Genomics
database
summary
IntroVerse
Garcia-Ruiz, Sonia; Gustavsson, Emil; Zhang, David; Reynolds, Regina; Chen, Zhongbo; Fairbrother-Browne, Aine; Gil-MartÃnez, Ana Luisa; BotÃa, Juan; Collado-Torres, Leonardo; Ryten, Mina
Introns and splicing errors/noise
database
summary
InvFEST
CÃƒÂ¡ceres, Mario; MartÃƒÂnez-Fundichely, Alexander; Casillas, SÃƒÂ²nia; Egea, Raquel; RÃƒÂ mia, Miquel; Barbadilla, Antonio; Puig, Marta
Polymorphic inversions in the human genome
database
summary
ipaQTL
Li, Lei; Ma, Xuelian; Cheng, Shumin; Ding, Ruofan; Zhao, Zhaozhao; Zou, Xudong; Guang, Shouhong; Wang, Qixuan; Yu, Chen; Ni, Ting
Intronic polyadenylation quantitative trait loci
database
summary
iPAVS
Pradeep Kumar Sreenivasaiah
Integrated Pathway Analysis and Visualization System
database
summary
IPD - Immuno Polymorphism Database
Marsh, Steven; Robinson, James; Halliwell, Jason; Hayhurst, James; Flicek, Paul; Parham, Peter
The Immuno-Polymorphism Database
database
summary
IPD-ESTDAB
Robinson J., Waller M.J., Marsh S.G.E.
Immunologically characterised melanoma cell lines
database
summary
IPD-HPA - Human Platelet Antigens
Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of human platelet antigens
database
summary
IPD-IMGT/HLA
Robinson, James; Barker, Dominic; Maccari, Giuseppe; Georgiou, Xenia; Cooper, Michael; Flicek, Paul; Marsh, Steven
The IPD-IMGT/HLA Database
database
summary
IPD-KIR - Killer-cell Immunoglobulin-like Receptors
Robinson J., Waller M.J., Marsh S.G.E.
Immuno polymorphism of killer-cell Ig-like receptors
database
summary
IPD-MHC
Robinson J., Waller M.J., Marsh S.G.E.
Sequences of the major histocompatibility complex
database
summary
iPfam
Finn, Robert; Miller, Benjamin; Clements, Jody; Bateman, Alex
A database of Pfam domain interactions
database
summary
IPI - International Protein Index
Kersey, P.J., Duarte, J., Apweiler, R.
Non-redundant sets of human, mouse and rat proteins
database
summary
iPPI-DB
Sperandio, Olivier; LabbÃ©, CÃ©line; Kuenemann, MÃ©laine; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry; Lagorce, David; Miteva, Maria; Villoutreix, Bruno
Inhibitors of protein-protein interactions
database
summary
iProClass
Wu, C.H.
, Huang, H.
, Chen, Y.
, Barker, W.C.
Annotated protein database with family, function, and structure information
database
summary
iProLINK
Hu Z.Z. and Wu C.H.
Annotated literature sources for protein features and names
database
summary
iProX
Zhu, Yunping; Chen, Tao ,; Ma, Jie; Liu, Yi; Chen, Zhiguang; Xiao, Nong; Lu, Yutong; Fu, Yinjin; Yang, Chunyuan; Li, Mansheng; Wu, Songfeng; Wang, Xue; Li, Dongsheng; He, Fuchu; Hermjakob, Henning
iProX in 2021: Connecting proteomics data sharing with big data
database
summary
iPTMnet
Huang, Hongzhan; Arighi, Cecilia; Ross, Karen; Ren, Jia; Li, Gang; Chen, Sheng-Chih; Cowart, Julie; Wang, Qinghua.; Vijay-Shanker, K; Wu, Cathy
No description supplied
database
summary
IRESite
Mokrejs M.
1,2
, Vopalensky V.
, Kolenaty O.
, Masek T.
, Feketova Z.
, Sekyrova P.
, Skaloudova B.
, Kriz V.
and Pospisek M.
1,5
Experimentally studied internal ribosome entry sites
database
summary
Iridovirus Comprehensive Database
Mincong Liang; Weiqiang Pan; Zhengqi Feng; Yangchi Cui; Hualong Su; Changjun Guo; Jianguo He
IVCDB: a comprehensive database of iridoviruses for epidemiology, genetics and functional genomics
database
summary
ISED
Yang, I.S.
1,2
, Lee, J.-L.
, Lee, J.S.
, Mitchell, W.P.
3,4
, Oh, H.-B.
, Kang, C.
, and Kim, K.H.
Influenza virus Sequence and Epitope Database
database
summary
Isfinder
Siguier P.
, Perochon J.
, Lestrade L.
, Mahillon J.
and Chandler M.
A database of bacterial Insertion Sequences
database
summary
Isobase
Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, and Bonnie Berger
IsoRank PPI Network Alignment Based Ortholog Database
database
summary
isomiRdb
Aparicio-Puerta, Ernesto; Hirsch, Pascal; Schmartz, Georges; Fehlmann, Tobias; Keller, Verena; Engel, Annika; Kern, Fabian; Hackenberg, Michael; Keller, Andreas
microRNA isoform expression
database
summary
iSyTE
Lachke, Salil; kakrana, Atul; Yang, Andrian; Anand, Deepti; Djordjevic, Djordje; Ramachandruni, Deepti; Singh, Abhyudai; Huang, Hongzhan; Ho, Joshua
No description supplied
database
summary
ITS2
Predicted structures of internal transcribed spacer 2 (ITS2)
database
summary
ITSoneDB
Pesole, Graziano; Santamaria, Monica; Fosso, Bruno; Licciulli, Vito Flavio; Balech, Bachir; Larini, Italia; Grillo, Giorgio; De Caro, Giorgio; Liuni, Sabino
No description supplied
database
summary
ITTACA
Elfilali A.
1,2
, Lair S.
1,2
, Verbeke C.
1,2
, La Rosa P.
, Radvanyi F.
and Barillot E.
1,2
ITTACA : Integrated Tumor Transcriptome Array and Clinical data Analysis
database
summary
IUBMB Nomenclature database
Gerard P. Moss
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
database
summary
IUPAC Nomenclature database
Gerard P. Moss
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
database
summary
IUPHAR/BPS Guide to Pharmacology
Jianfeng Jiang; et al.
The IUPHAR/BPS Guide to PHARMACOLOGY in 2026
database
summary
IUPHAR/BPS Guide to Pharmacology
Simon D Harding, Jane F Armstrong, Elena Faccenda, Christopher Southan, Stephen P H Alexander, Anthony P Davenport, Michael Spedding, Jamie A Davies
Properties of established and potential drug targets: GPCRs, ion channels, nuclear hormone receptors, catalytic receptors, transporters and enzymes
database
summary
IUPHAR/BPS Guide to Pharmacology
Harding, Simon D; Sharman, Joanna L; Faccenda, Elena; Southan, Christopher; Pawson, Adam J; Ireland, Sam; Gray, Alasdair JG; Bruce, Liam; Alexander, Stephen PH; Anderton, Stephen; Bryant, Claire; Davenport, Anthony P; Doerig, Christian; Fabbro, Doriano; Levi-Schaffer, Francesca; Spedding, Michael; Davies, Jamie A
Properties of established and potential drug targets: GPCRs, ion channels, nuclear hormone receptors, catalytic receptors, transporters and enzymes
database
summary
IUPHAR/BPS Guide to Pharmacology
Harding, Simon; Armstrong, Jane; Faccenda, Elena; Southan, Christopher; Alexander, Stephen PH; Davenport, Anthony; Pawson, Adam; Spedding, Michael; Davies, Jamie
The IUPHAR/BPS Guide to PHARMACOLOGY in 2022: curating pharmacology for COV
database
summary
iUUCD
Xue, Yu; Zhou, Jiaqi; Xu, Yang ,; Lin, Shaofeng; Guo, Yaping; Deng, Wankun; Zhang, Ying.; Guo, Anyuan
The ubiquitin and ubiquitin-like (Ub/Ubl) conjugation is one of the most im
database
summary
iUUCD
Zexian Liu
Integrated Ubiquitin and ubiquitin-like conjugation database
database
summary
IVDB - Influenza Virus Database
Chang S.
1,2
, Zhang J.
, Liao X.
, Zhu X.
1,3
, Wang D.
, Zhu J.
, Feng T.
, Yang H.
, Yu J.
and Wang J.
Annotated sequences and geographic distribution of the influenza virus
database
summary
JAIL
Structure-based interface library for macromolecules
database
summary
JASPAR
Fornes, Oriol;Castro-Mondragon, Jaime A;Khan, Aziz;vanÃ‚Â derÃ‚Â Lee, Robin;Zhang, Xi;Richmond, Phillip A;Modi, Bhavi P;Correard, Solenne;Gheorghe, Marius;BaranaÃ…Â¡iÃ„â€¡, Damir;Santana-Garcia, Walter;Tan, Ge;ChÃƒÂ¨neby, Jeanne;Ballester, Benoit;Parcy, FranÃƒÂ§ois;Sandelin, Albin;Lenhard, Boris;Wasserman, Wyeth W;Mathelier, Anthony
No description supplied
database
summary
JASPAR
Mathelier, Anthony; Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-MondragÃƒÂ³n, Jaime; van der Lee, Robin; Bessy, Adrien; ChÃƒÂ¨neby, Jeanne; Kulkarni, Shubhada; Tan, Ge,; Baranasic, Damir; Arenillas, David; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoit; Wasserman, Wyeth; Parcy, FranÃƒÂ§ois
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
database
summary
JASPAR
Mathelier, Anthony; Castro-Mondragon, Jaime; Riudavets Puig, Rafael; Rauluseviciute, Ieva; Berhanu Lemma, Roza; Turchi, Laura; Blanc Mathieu, Romain; LUCAS, Jeremy; Boddie, Paul; Khan, Aziz; Manosalva Perez, Nicolas; Fornes, Oriol; Leung, Tiffany; Aguirre
JASPAR 2022: the 9th release of the open-access database of transcription f
database
summary
JASPAR
Mathelier, Anthony; Rauluseviciute, Ieva; Riudavets Puig, Rafael; Blanc Mathieu, Romain; Castro-Mondragon, Jaime; Ferenc, Katalin; Kumar, Vipin; Berhanu Lemma, Roza; LUCAS, Jeremy; ChÃ¨neby, Jeanne; Baranasic, Damir; Khan, Aziz; Fornes, Oriol; Gundersen, S
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
database
summary
Jenalib: Jena Library of Biological Macromolecules
Reichert, J., Suehnel, J.
Visualization and analysis of 3D biopolymer structures
database
summary
JET2 Viewer
Ripoche, Hugues,; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra
Joint Evolutionary Trees: Protein-protein interaction patches in known structures
database
summary
JMorp
Kinoshita, Kengo; Tadaka, Shu; Hishinuma, Eiji; Komaki, Shohei; Motoike, Ikuko; Kawashima, Junko; Saigusa, Daisuke; Inoue, Jin; Takayama, Jun; Okamura, Yasunobu; Aoki, Yuichi; Shirota, Matsuyuki; Otsuki, Akihito; Katsuoka, Fumiki; Shimizu, Atsushi; Tamiya
Japanese Multi Omics Reference Panel
database
summary
jMorp
Kinoshita, Kengo; Tadaka, Shu; Kawashima, Junko; Hishinuma, Eiji; Saito, Sakae; Okamura, Yasunobu; Otsuki, Akihito; Kojima, Kaname; Komaki, Shohei; Aoki, Yuichi; Kanno, Takanari; Saigusa, Daisuke; Inoue, Jin; Shirota, Matsuyuki; Takayama, Jun; Katsuoka, Fumiki; Shimizu, Atsushi; Tamiya, Gen; Shimizu, Ritsuko; Hiratsuka, Masahiro; Motoike, Ikuko; Koshiba, Seizo; Sasaki, Makoto; Yamamoto, Masayuki,
jMorp: Japanese Multi-Omics Reference Panel update report 2023
database
summary
JoGO
Masao Nagasaki; et al.
JoGO 1.0: a long-read human ACGT-haplotype database covering 4.17 million non-redundant variants
database
summary
jPOST
Okuda, Shujiro; Watanabe, Yu; Moriya, Yuki.; Kawano, Shin; Yamamoto, Tadashi; Matsumoto, Masaki; Takami, Tomoyo; Kobayashi, Daiki; Araki, Norie; Yoshizawa, Akiyasu.; Tabata, Tsuyoshi; Sugiyama, Naoyuki; Goto, Susumu; Ishihama, Yasushi
Japanese ProteOme Standard repository
database
summary
JuncDB
Carmel, Liran; Chorev, Michal; Guy, Lotem
Exon-exon Junction database
database
summary
KaPPA-View
Kazusa Plant Pathway Viewer
database
summary
KaryotypeDB
Nenno M.
Karyotype and chromosome data for animal and plant species
database
summary
KBDOCK
Ritchie, David; Ghoorah, Anisah; Devignes, Marie-Dominique; Smail-Tabbone, Malika
Protein domain interactions and interfaces
database
summary
KBERG
Tang S.
, Zhang Z.
, Tan S.L.
, Tang M.-H.E.
, Kumar A.P.
, Ramadoss S.K.
, and Bajic V.B.
KnowledgeBase for Estrogen Responsive Genes
database
summary
KEGG
Minoru Kanehisa
Kyoto encyclopedia of genes and genomes: databases on genes, proteins, and metabolic pathways
database
summary
KEGG
Kanehisa, Minoru; Furumichi, Miho; Sato, Yoko,; Kawashima, Masayuki; Ishiguro-Watanabe, Mari
Kyoto encyclopedia of genes and genomes: databases on genes, proteins, and metabolic pathways
database
summary
KERIS
xiao, wenzhong; Li, Peng .; Tompkins, Ronald
Kaleidoscope of gEne Responses to Inflammation among Species
database
summary
KIDFamMap
Jinn-Moon Yang
Kinase-inhibitor-disease family map
database
summary
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space
Rahman, Rayees;Ung, Peter Man-Un;Schlessinger, Avner
No description supplied
database
summary
KinaseMD
Zhao, Zhongming; Hu, Ruifeng; Xu, Haodong; Jia, Peilin
Kinase Mutations and Drug responses
database
summary
Kincore
Dunbrack, Roland; Modi, Vivek
Protein kinase sequence, structure and phylogeny
database
summary
KineticDB
Bogatyreva, N.S.
, Osypov, A.A.
, Ivankov, D.N.
Kinetic data on folding of single-domain globular proteins
database
summary
KinG: Kinases in Genomes
Malini Manoharan
, Priyanka Sharma
, Chintalapati Janaki
1,2
, Shashi Shekhar
, Narayanaswamy Srinivasan
, Ramaswamy Rakshambikai
KinG: Kinases in Genomes is a comprehensive collection of Ser/Thr/Tyr specific protein kinases and similar sequences encoded in the completed genomes of eukaryotes and prokaryotes. This site provides a detailed classification based on sequence similarity between catalytic domains of protein kinases.
database
summary
Kinomer
Classification of protein kinases encoded in various eukatotic species
database
summary
KLIFs
Kinase-ligand Interaction Fingerprints and Structures
database
summary
KnockRBP
Yungang Xu; et al.
KnockRBP: an integrated multi-omics database of functional perturbations for RNA binding proteins
database
summary
KnockTF
Feng, Chenchen;Song, Chao;Liu, Yuejuan;Qian, Fengcui;Gao, Yu;Ning, Ziyu;Wang, Qiuyu;Jiang, Yong;Li, Yanyu;Li, Meng;Chen, Jiaxin;Zhang, Jian;Li, Chunquan
Transcription factors (TFs) and their target genes have important functions
database
summary
KnockTF
Li, Chunquan; Feng, Chenchen; Song, Chao; Song, Shuang; Zhang, Guorui; Yin, Mingxue; Zhang, Yue-Xin; Qian, Feng-Cui; Wang, Qiuyu; Guo, Maozu
KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multi-species
database
summary
KnotProt
Sulkowska, Joanna; Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric; Stasiak, Andrzej; Millett, Kenneth; SuÃ…â€škowski, Piotr
Proteins with Topological knots and slipknots
database
summary
KnotProt 2.0: a database of proteins with knots and other entangled structures
Dabrowski-Tumanski, Pawel;Rubach, Pawel;Goundaroulis, Dimos;Dorier, Julien;SuÃ…â€škowski, Piotr;Millett, Kenneth C;Rawdon, Eric J;Stasiak, Andrzej;Sulkowska, Joanna I
No description supplied
database
summary
KNOTTIN
Gelly, Jean-Christophe; Postic, Guillaume; Gracy, JÃƒÂ©rÃƒÂ´me; PÃƒÂ©rin, Charlotte; Chiche, Laurent
No description supplied
database
summary
Knottin database
Database of knottins - small proteins with an unusual "disulfide through disulfide" knot
database
summary
KUPS
Xue-wen Chen
1,2
, Jong Cheol Jeong
and Patrick Dermyer
Interacting and non-interacting protein pairs
database
summary
L1Base
Functional annotation and prediction of LINE-1 elements
database
summary
Laminin Database
Daiane C. F. Golbert, Leandra Linhares-Lacerda, Luiz G. Almeida, Eliane Correa-de-Santana, Alice R. de Oliveira, Alex S. Mundstein, Wilson Savino and Ana T. R. de Vasconcelos
Laminin Database
database
summary
LAMP
Achchuthan Shanmugasundram
1,2,*
, Faviel F Gonzalez-Galarza
, Jonathan Wastling
, Olga Vasieva
and Andrew R Jones
Library of Apicomplexan Metabolic Pathways (LAMP): A manually curated database for metabolic pathways of apicomplexan parasites
database
summary
Leaf Senescence Database
Luo, Jingchu; Li, Zhonghai; Zhao, Yi.; Liu, Xiaochun; Peng, Junying; Guo, Hongwei
Leaf Senescence Database
database
summary
LEGER
Dieterich G., KÄrst U., Fischer E., Wehland J. and JÄnsch L.
Comparative genomics of pathogenic and non-pathogenic
Listeria
spp.
database
summary
LegumelIP
Zhao, Patrick; Dai, Xinbin; Zhuang, Zhaohong; Boschiero, Clarissa; Dong, Yibo
Model Legumes Integrative database Platform
database
summary
LenVarDB
Sowdhamini, Ramanathan; Mutt, Eshita; Mathew, Oommen
Database of length variantion in protein domains
database
summary
LeptoList
CÃƒÂ©dric Cabau
, Virginie Cubas
, Gang Fang
1,3
, Christine Ho
, Zhou Yu
, Ivan Moszer
2,3
, Antoine Danchin
1,3
Leptospira interrogans
genome database
database
summary
LIFEdb
Mehrle A.
, Rosenfelder H.
, Schupp I.
, del Val C.
, Arlt D.
, Hahne F.
, Bechtel S.
, Simpson J.
, Hofman O.
, Winston Hide W.
, Glatting K.-H.
, Huber W.
, Pepperkok R.
, Poustka A.
and Wiemann S.
A database on localization, interaction, functional assays and expression of human proteins
database
summary
LigAsite
LigASite database of binding sites
database
summary
LINCS Data Portal
Schurer, Stephan; Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel; Turner, John; Vidovic, DuÃ…Â¡ica; Forlin, Michele; Kelley, Tanya; DÃ¢â‚¬â„¢Urso, Alessandro; Allen, Bryce; Torre, Denis; Jagodnik, Kathleen; Wang, Lily; Jenkins, Sherry; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma'ayan, Avi; Pillai, Ajay
No description supplied
database
summary
LincSNP
Ning, Shangwei; Gao, Yue; Li, Xin,; Shang, Shipeng; Guo, Shuang; Sun, Dailin; Gan, Jing; Sun, Jie; Zhang, Yakun; Wang, Junwei; Wang, Xinyue; Li, Xia; Zhang, Yunpeng
Association of human lncRNAs with disease-related SNPs
database
summary
Lineage Landscape
Liu, Guang-Hui (proxy) (contact); Yan, Haoteng; Wang, Ronghao; Ma, Shuai; Huang, Daoran; Wang, Si; REN, JIE; ZHANG, WEIQI; qu, jing; Zhou, Yuanchun
Omics of lineage determination in animals
database
summary
LinkedOmics
Zhang, Bing; Vasaikar, Suhas; Straub, Peter; Wang, Jing,,
No description supplied
database
summary
LinkProt
Sulkowska, Joanna; Dabrowski-Tumanski, Pawel; Jarmolinska, Aleksandra; Niemyska, Wanda; Rawdon, Eric; Millett, Kenneth
Topologically non-trivial protein structures made by single, double, or triple chains
database
summary
Lipase Engineering Database
Fischer, M., Pleiss, J.
Integrated information on sequence, structure, and function of lipases and esterases
database
summary
Lipid MAPS
Cotter D.1, Maer A.
, Guda C.
, Saunders B.
, and Subramaniam S.
1,3
Lipid-associated proteins
database
summary
LIPID MAPS
Conroy, Matthew; Andrews, Robert; Andrews, Simon; Cockayne, Lauren; Dennis, Edward; Fahy, Eoin; Gaud, Caroline; Griffiths, William; Jukes, George; Kolchin, Maksim; Mendivelso, Karla; Lopez, Andrea; Ready, Caroline; Subramaniam, Shankar; O'Donnell, Valerie
LIPID MAPS: Update to databases and tools for the lipidomics community.
database
summary
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies
Aparicio-Puerta, Ernesto;JÃƒÂ¡spez, David;LebrÃƒÂ³n, Ricardo;Koppers-Lalic, Danijela;Marchal, JuanÃ‚Â A;Hackenberg, Michael
No description supplied
database
summary
LIRBase
Jia, Lihua; Li, Yang; Huang, Fangfang; Jiang, Yingru; Li, Haoran; Wang, Zhizhan; Chen, Tiantian; Li, Jiaming; Zhang, Zhang; Yao, Wen
National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China; National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
yaowen@henau.edu.cn
Long Inverted Repeats in eukaryotes
LIRBase is a specialized database of 6,619,473 long inverted repeats (LIRs) identified in 424 eukaryotic genomes, including 297,317 LIRs in 77 invertebrate metazoa genomes, 1,731,978 LIRs in 139 plant genomes, and 4,590,178 LIRs in 208 vertebrate genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.
Long Inverted Repeats in eukaryotes
database
summary
LitCovid
Lu, Zhiyong; Chen, Qingyu; Allot, Alexis
Curated COVID-19 literature
database
summary
LitCovid
Chen, Qingyu; Allot, Alexis; Leaman, Robert; Wei, Chih- Hsuan; Aghaarabi, Elaheh; Guerrerio, John; Xu, Lilly; Lu, Zhiyong
LitCovid in 2022: an information resource for the COVID-19 literature
database
summary
LLPSDB: a database of proteins undergoing liquidÃ¢â‚¬â€œliquid phase separation in vitro
Li, Qian;Peng, Xiaojun;Li, Yuanqing;Tang, Wenqin;Zhu, JiaÃ¢â‚¬â„¢an;Huang, Jing;Qi, Yifei;Zhang, Zhuqing
No description supplied
database
summary
lnc2cancer
Li, Xia; Gao, Yue; Shang, Shipeng; Guo, Shuang; Li, Xin,; Zhou, Hanxiao; Liu, Hongjia; Sun, Yue; Wang, Junwei; Wang, Peng; Zhi, Hui'; Ning, Shangwei; Zhang, Yunpeng
Lnc2Cancer 3.0 includes comprehensive data on experimentally supported long
database
summary
Lnc2Meth
Li, Xia; Zhi, Hui'; Li, Xin,; Wang, Peng,.; Gao, Yue'; Gao, Baoqing; Zhou, Dianshuang; Zhang, Yan *; Guo, Maoni; Yue, Ming; Shen, Weitao; Ning, Shangwei; Jin, Lianhong
No description supplied
database
summary
LncACTdb
Li, Xia; Wang, Peng; Guo, Qiuyan.; Qi, Yue; Hao, Yangyang2; Gao, Yue; Zhi, Hui; Zhang, Yuanfu; Sun, Yue; Zhang, Yakun; Xin, Mengyu; zhang, Yunpeng`; Ning, Shangwei
LncACTdb 3.0: an updated database of experimentally supported ceRNA interac
database
summary
LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments
Wang, Peng;Li, Xin;Gao, Yue;Guo, Qiuyan;Wang, Yanxia;Fang, Ying;Ma, Xueyan;Zhi, Hui;Zhou, Dianshuang;Shen, Weitao;Liu, Weisha;Wang, Lihua;Zhang, Yunpeng;Ning, Shangwei;Li, Xia
No description supplied
database
summary
LncBook
Li, Zhao; Liu, Lin; Feng, Changrui; Qin, Yuxin; Xiao, Jingfa,; Zhang, Zhang; Ma, Lina
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annota
database
summary
LncBook: a curated knowledgebase of human long non-coding RNAs
Ma, Lina;Cao, Jiabao;Liu, Lin;Du, Qiang;Li, Zhao;Zou, Dong;Bajic, Vladimir B;Zhang, Zhang
No description supplied
database
summary
LnCeCell
Shangwei Ning
LnCeCell is a comprehensive resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data
database
summary
LnCeCell
Li, Xia; Wang, Peng; Guo, Qiuyan.; Hao, Yangyang; Liu, Qian; Gao, Yue'; Zhi, Hui'; Li, Xin,; Shang, Shipeng; Guo, Shuang; zhang, Yunpeng`; Ning, Shangwei
lncRNA-associated ceRNA networks
database
summary
LNCediting
Gong, Jing; Liu, Chun-Jie; Liu, Wei; Xiang, Yu; Diao, Lixia; Guo, An-Yuan; Han, Leng
RNA editing sites in lncRNAs from human, monkey, mouse and fly
database
summary
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation
Wang, Peng;Li, Xin;Gao, Yue;Guo, Qiuyan;Ning, Shangwei;Zhang, Yunpeng;Shang, Shipeng;Wang, Junwei;Wang, Yanxia;Zhi, Hui;Fang, Ying;Shen, Weitao;Zhang, Guangmei;Chen, Steven Xi;Li, Xia
No description supplied
database
summary
LncExpDB
Ma, Lina; Li, Zhao; Liu, Lin; Jiang, Shuai; Li, Qianpeng; Feng, Changrui; Du, Qiang; Zou, Dong; Xiao, Jingfa; Zhang, Zhang
Human lncRNA expression database
database
summary
LNCipedia
Mestdagh, Pieter; Volders, Pieter-Jan; Verheggen, Kenneth; Menschaert, Gerben; Vandepoele, Klaas; Martens, Lennart; Vandesompele, Jo
Human lncRNA gene sequences and structures
database
summary
LNCipedia 5: towards a reference set of human long non-coding RNAs
Volders, Pieter-Jan;Anckaert, Jasper;Verheggen, Kenneth;Nuytens, Justine;Martens, Lennart;Mestdagh, Pieter;Vandesompele, Jo
No description supplied
database
summary
LncPepAtlas
Liang Sun
Long Non-Coding RNA Peptide Atlas
database
summary
LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse
Cheng, Liang;Wang, Pingping;Tian, Rui;Wang, Song;Guo, Qinghua;Luo, Meng;Zhou, Wenyang;Liu, Guiyou;Jiang, Huijie;Jiang, Qinghua
No description supplied
database
summary
lncRNAdb
Quek, Xiu Cheng; Thomson, Daniel; Maag, Jesper; Gloss, Brian; Bartonicek, Nenad; Signal, Bethany; Clark, Michael; Dinger, Marcel
Long Non-Coding RNA Database
database
summary
LncRNADisease
Geng Chen
1,2,3#
, Ziyun Wang
2#
, Dongqing Wang
2#
, Chengxiang Qiu
, Mingxi Liu
, Xing Chen
, Qipeng Zhang
, Guiying Yan4
, and Qinghua Cui
1,2,3*
LncRNADisease: a database for long noncoding RNA associated diseases
database
summary
lncRNAfunc
Zhou, Xiaobo; Yang, Mengyuan; Lu, Huifen; Liu, Jiajia; Wu, Sijia; Kim, Pora
Regulatory roles of lncRNAs in cancer
database
summary
lncRNASNP
Gong, Jing; Yang, Yanbo; Wang, Dongyang; Miao, Ya-Ru; Wu, Xiaohong; Luo, Haohui; Cao, Wen; Yang, Wenqian; Yang, Jianye; Guo, Anyuan
lncRNASNP v3: an updated database for functional variants in long non-codin
database
summary
lncRNASNP
Guo, An-Yuan; Gong, Jing; Liu, Wei.; Zhang, Jiayou; Miao, Xiaoping
SNPs in human lncRNAs
database
summary
lncRNASNP2
Guo, An-Yuan; Miao, Yaru; Liu, Wei.; Zhang, Qiong
No description supplied
database
summary
LncRNAWiki
Ma, Lina; Li, Ang; Zou, Dong; Yu, Jun; Bajic, Vladimir; Zhang, Zhang
Community-curated database of human lncRNAs
database
summary
LncRNAWiki
Ma, Lina; Liu, Lin; Li, Zhao; Liu, Chang; Zou, Dong; Li, Qianpeng; Feng, Changrui; Jing, Wei; Luo, Sicheng; Zhang, Zhang
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced
database
summary
LncSEA
Li, Chunquan; Chen, Jiaxin; Zhang, Jian.,; Gao, Yu; Li, Yanyu; Feng, Chenchen; Song, Chao; Ning, Ziyu; Zhou, Xinyuan; Zhao, Jianmei; Feng, Minghong; Zhang, Yue-Xin; Wei, Ling; Pan, QI; Jiang, Yong'; Qian, Feng-Cui; Han, Junwei.; Yang, YongSan; Wang, Qiuyu
Reference human lncRNA sets
database
summary
LncSEA
Wang, Qiuyu; Zhang, Guorui; Song, Chao; Fan, Shifan; Yin, Mingxue; Wang, Xinyue; Zhang, Yuexin2; Huang, Xuemei; Li, Ye; Shang, Desi; Li, Chunquan
LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis
database
summary
lncTarD
Wang, Li; Zhao, Hongying; Yin, Xiangzhe; Xu, Haotian; Liu, Kailai; Liu, Wangyang; Wang, Lixia; Zhang, Caiyu; Bo, Lin; Lan, Xicheng; Lin, Shihua; Feng, Ke; Ning, Shangwei; zhang, Yunpeng`
LncTarD 2.0: an updated comprehensive database for experimentally-supported
database
summary
LncTarD: a manually-curated database of experimentally-supported functional lncRNAÃ¢â‚¬â€œtarget regulations in human diseases
Zhao, Hongying;Shi, Jian;Zhang, Yunpeng;Xie, Aimin;Yu, Lei;Zhang, Caiyu;Lei, Junjie;Xu, Haotian;Leng, Zhijun;Li, Tengyue;Huang, Waidong;Lin, Shihua;Wang, Li;Xiao, Yun;Li, Xia
No description supplied
database
summary
LOCATE
Fink J.L.
1,2
, Aturaliya R.N.
1,2
, Davis M.J.
, Zhang F.
, Hanson K.
1,2
, Teasdale M.S.
, Kai C.
, Kawai, J.
3,4
, Carninci P.
3,4
, Hayashizaki Y.
3,4
and Teasdale R.D.
1,2
Subcellular localization of mouse proteins
database
summary
LocDB
Shruti Rastogi
, and Burkhard Rost
1,2,3
Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
database
summary
Locus Reference Genomic sequences
Cunningham, Fiona; MacArthur, Jacqueline; Morales, Joannella; Tully, Ray; Astashyn, Alex; Gil, Laurent; Bruford, Elspeth; Dalgleish, Raymond; Larsson, Pontus; Flicek, Paul; Maglott, Donna
Each LRG is stable genomic DNA sequence for a region of the human genome
database
summary
LOQATE
Schuldiner, Maya; Breker, Michal; Moldavski, Ofer; Gymrek, Melissa
Localization and Quantitation Atlas of the Yeast Proteome
database
summary
Lowe Syndrome Mutation Database [Retired]
Mutations in the OCRL1 gene encoding phosphatidylinositol-4,5-bisphosphate 5-phosphatase
database
summary
LOX-DB
LÜtteke, T.
, Krieg, P.
, FÜrstenberger, G.
, von der Lieth, C.-W.
Mammalian, invertebrate, plant and fungal lipoxygenases
database
summary
LPFC
Library of protein family core structures
database
summary
LPSN
Meier-Kolthoff, Jan; SardÃ Carbasse, Joaquim; Peinado-Olarte, Rosa L.; GÃ¶ker, Markus
List of Prokaryotic names with Standing in Nomenclature and Type Strain Genome Server
database
summary
LPSN
Parte, Aidan
List of Prokaryotic names with Standing in Nomenclature
database
summary
LUCApedia
Laura Landweber
Predicted genome, proteome, and reactome of LUCA
database
summary
LumbriBASE
ESTs of the earthworm
Lumbricus rubellus
database
summary
Lynx: a database and knowledge extraction engine for integrative medicine
Sulakhe, Dinanath (contact); Xie, Bingqing; Taylor, Andrew; D'Souza, Mark; Balasubramanian, Sandhya; Hashemifar, Somaye; White, Steven; Dave, Utpal; Agam, Gady; Xu, Jinbo; Wang, Sheng; Gilliam, Conrad; Maltsev, Natalia
Genomic and clinical data on complex heritable disorders
database
summary
M-CSA
Ribeiro, Antonio; Holliday, Gemma; Furnham, Nicholas; Tyzack, Jonathan; Ferris, Katherine; Thornton, Janet
M-CSA is a database of enzyme reaction mechanisms. It provides annotation o
database
summary
M2OR
Topin, JÃ©rÃ©mie; Lalis, Maxence; HladiÅ¡, Matej; Briand, LoÃ¯c; Fiorucci, SÃ©bastien
M2OR: A Database of Olfactory Receptor-Odorant Pairs for Understanding the Molecular Mechanisms of Olfaction
database
summary
M3D
Many Microbe Microarrays Database
database
summary
m5C-Atlas
Chen, Kunqi; Ma, Jiongming; Song, Bowen; Wei, Zhen.; Huang, Daiyun; Zhang, Yuxin; Su, Jionglong; MagalhÃ£es, JoÃ£o Pedro de; Rigden, Daniel J.; Meng, Jia
The 5-methylcytosine (m5C) epitranscriptome
database
summary
m6A-Atlas
Chen, Kunqi; Lu, Zhi-Liang; MagalhÃƒÂ£es, JoÃƒÂ£o Pedro de; Meng, Jia; Rong, Rong; Song, Bowen; Su, Jionglong; Tang, Yujiao; Wei, Zhen.; Wu, Xiangyu; Xu, Qingru; Ma, Jiongming; Liu, Gang; Rigden, Daniel J.
The N6-methyladenosine (m6A) epitranscriptome including base-resolution data
database
summary
m6A-Atlas
Chen, Kunqi; Liang, Zhanmin; Ye, Haokai; Ma, Jiongming; Wei, Zhen; Wang, Yue; Zhang, Yuxin2; huang, daiyun; Song, Bowen; Meng, Jia; Rigden, Daniel J.
m6A-Atlas v2.0: updated resources for unravelling the N6-methyladenosine (m6A) epitranscriptome among multiple species
database
summary
m6AConquer
Wei, Zhen; Yang, Shiqi; Wang, Xiaoyang; Wang, Jingshu; Li, Ruohan; Wei, Jialiang; et al.
m6AConquer: a consistently quantified and orthogonally validated database for m6A-driven transcriptome remodeling in cancer
database
summary
M6AREG
Chong Qin; et al.
m6AREG: a comprehensive database of m6A regulatory variants and their roles in diseases
database
summary
M6AREG
Liu, Shuiping; CHEN, Lu; ZHANG, Yintao; ZHOU, Ying; HE, Ying; Chen, Zhen; QI, Shasha; ZHU, Jinyu; CHEN, Xudong; ZHANG, Hao; Luo, Yongchao; Tao, Lin; Zhu, Feng
m6A vs disease and drug response
database
summary
m6AVar
Ren, Jian; Zheng, Yueyuan; Nie, Peng; Peng, Di; He, Zhihao; Liu, Mengni; Xie, Yubin; Miao, Yanyan; Zuo, Zhixiang
No description supplied
database
summary
m7GHub
Song, Bowen; Wang, Xuan; Zhang, Yuxin2; Chen, Kunqi; Liang, Zhanmin; Ma, Jiongming; Xia, Rong; de MagalhÃ£es, JoÃ£o Pedro; Rigden, Daniel J.; Meng, Jia
m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m7G) epitranscriptome
database
summary
MACC
Cao, Zhiwei; Gao, Jian; Mo, Saifeng; Wang, Jun; Zhang, Mou; Shi, Yao; Zhu, Chuhan; Shang, Yuxuan; Tang, Xinyue; Zhang, Shiyue; Wu, Xinwen; Xu, Xinyan; Wang, Yiheng; Li, Zihao; Zheng, Genhui; Chen, Zikun; Wang, Qiming; Tang, KaiLin,
MACC: A Visual Interactive Knowledgebase of Metabolite-Associated Cell Communications
database
summary
MachiBase
Drosophila melanogaster 5' mRNA transcription start site database
database
summary
MACiE
Holliday, Gemma
; Andreini, Claudia
2,3
; Fischer, Julia
; Rahman, Syed
; Almonacid, Daniel
; Williams, Sophie
and Pearson, William
Mechanism, Annotation and Classification in Enzymes
database
summary
MacrocycleDB
Zhongxu Zhou; et al.
MacrocycleDB: a comprehensive database of macrocyclic compounds for drug discovery
database
summary
MaizeGDB
Lawrence, C.J.
, Dong, Q.
, Polacco, M.L.
, Seigfried, T.E.
, Brendel, V.
1,2
Maize genetics and genomics database
database
summary
MAJIQlopedia
Quesnel-ValliÃ¨res, Mathieu; Jewell, San; Barash, Yoseph; Thomas-Tikhonenko, Andrei; Lynch, Kristen
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer
database
summary
MalaCards
Rappaport, Noa; Twik, Michal; Plaschkes, Inbar; Nudel, Ron; Iny Stein, Tsippi; Levitt, Jacob; Gershoni, Moran; Morrey, C; Safran, Marilyn; Lancet, Doron
Human maladies and their annotations, organized into "disease cards"
database
summary
MALISAM
Manual alignments for structurally analogous motifs in proteins
database
summary
MAMEP - Molecular Anatomy of the Mouse Embryo Project
Gene expression data on mouse embryos
database
summary
MAMI
Zhao, Fangqing; Zhou, Tian; Xiao, Liwen; Zuo, Zhenqiang
MAMI: a comprehensive database of mother-infant microbiome and probiotic resources
database
summary
Mammalian Gene Collection
Full-length open reading frame clones for human, mouse, and rat genes
database
summary
MamMiBase
de Vasconcelos A.T.R.
, GuimarÃes A.C.R.
, Castelletti C.H.M.
, Caruso C.S.
, Ribeiro C.
, Yokaichiya F.
, ArmÔa G.R.G.
, Pereira G.S.P.
, da Silva I.T.
, Schrago C.G.
, Fernandes A.L.V.
, da Silveira A.R.
, Carneiro A.G.
, Carvalho B.M.
, Viana C.J.M.
, Gramkow D.
, Lima F.J.
, CorrÊa L.G.G.
, Mudado M.A.
, Nehab-Hess P.
, de Souza R.
, CorrÊa R.L.
and Russo C.A.M.
Mammalian Mitochondrial genome database
database
summary
MamPol
Egea R.
, Casillas S.
, FernÃƒÂ¡ndez E.
, Senar MA.
and Barbadilla A.
Mammalia Polymorphism Database
database
summary
Manteia
Tassy, Olivier; PourquiÃƒÂ©, Olivier
Embryonic development of the mouse, chicken, zebrafish and human
database
summary
Manually Curated Database of Rice Proteins
Priyanka Garg, Rashmi Jain, Shaji V. Joseph, Akhilesh K. Tyagi, Saurabh Raghuvanshi
Manually curated database of rice proteins
database
summary
MAPbrain
Xiaoqun Wang
Multi-omics Atlas of the Primate Brain
database
summary
MAPPER
Alberto Riva
Putative transcription factor binding sites in various genomes
database
summary
MAPU
Gnad, F.
, Oroshi, M.
, Birney, E.
, Mann, M.
Max-Planck Unified Proteome Database
database
summary
markerDB
Wishart, David; Bartok, Brendan; Oler, Eponine; Liang, Kevin; Budinski, Zachary; Berjanskii, Mark; Guo, An Chi; Cao, Xuan; Wilson, Michael ,
Biomarkers: chemical, protein, chromosomal and genetic
database
summary
MASI
Chen, Yu Zong; Zeng, Xian; Yang, Xue; Fan, Jiajun; Tan, Ying'; Ju, Lingyi; Shen, Wanxiang; Wang, Yali.; Wang, Xinghao; Chen, Wei Ping; Ju, Dianwen
Microbiota - Active Substance Interactions database
database
summary
MAtDB2
MIPS
Arabidopsis thaliana
database
database
summary
MatrisomeDB
Alexandra Naba
The extracellular matrix (ECM) is a complex and dynamic meshwork of cross-l
database
summary
MatrixDB
Launay, Guillaume; Salza, Romain; Thierry-Mieg, Nicolas; RICARD-BLUM, Sylvie
Extracellular matrix proteins and their interactions
database
summary
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
Clerc, Olivier;Deniaud, Madeline;Vallet, Sylvain D;Naba, Alexandra;Rivet, Alain;Perez, Serge;Thierry-Mieg, Nicolas;Ricard-Blum, Sylvie
No description supplied
database
summary
MBGD - Microbial Genome Database
Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu
Microbial genome database for comparative analysis
database
summary
mBodyMap
Chen, Weihua; Jin, Hanbo; Hu, Guoru; Sun, Chuqing; Duan, Yiqian; ZHANG, Zhenmo; Zhao, Xing-Ming; Liu, Zhi,
Distribution of microbes across the human body in health and disease
database
summary
MDPD
Mutation Database for Parkinson's Disease
database
summary
MDRepo
Travis Wheeler
Molecular Dynamics simulations
database
summary
MeDAS
Chen, Lu; Li, Zhidan; Zhang, Yi-ming; Bush, Stephen J; Tang, Chao; Chen, Li; Zhang, Dan; Urrutia, Araxi; Lin, Jing-wen
Alternative splicing during development in 20 species
database
summary
MeDBA
Li, Guo-Bo; Yu, Jun-Lin; Wu, Song; Zhou, Cong; Dai, Qing-Qing; Schofield, Christopher
Metalloenzyme families, structures, ligands
database
summary
MediaAssist
Gadgil, Mugdha; et al.
MediaAssist: Database to support the design and optimization of cell culture media
database
summary
MediaDive
Koblitz, Julia; Halama, Philipp; Spring, Stefan; Thiel, Vera; Baschien, Christiane; Hahnke, Richard; Pester, Michael; Overmann, JÃ¶rg; Reimer, Lorenz
Culture media
database
summary
MeDIC
Leo Han; et al.
Medicines, Diseases, Indications, and Contraindications (MeDIC): A Foundation for Computational Drug Repurposing
database
summary
MeDReaders
Wang, Guohua; Luo, Ximei; Wang, Jianan; Wan, Jun.; Xia, Shuli; Zhu, Heng; Qian, Jiang; Wang, Yadong
No description supplied
database
summary
MegaMotifbase
Structural motifs in protein families and superfamilies
database
summary
MEGaRes
Boucher, Christina; Lakin, Steven; Dean, Chris; Noyes, Noelle; Dettenwanger, Adam; Ross, Annie; Doster, Enrique; Rovira, Pablo; Abdo, Zaid; Jones, Kenneth; Ruiz, Jaime; Belk, Keith; Morley, Paul
Mechanisms of antimicrobial resistance
database
summary
MegaRes
Bonin, Nathalie; Doster, Enrique; Worley, Hannah; Pinnell, Lee J.; Bravo, Jonathan E.; Ferm, Peter; Marini, Simone; Prosperi, Mattia; Noyes, Noelle; Morley, Paul S.; Boucher, Christina
MEGARes and AMR++, v3.0: An updated comprehensive database of antimicrobial
database
summary
MeGX
Lombardot T.
, Kottman R.
, Pfeffer H.
, Richter M.
, Teeling H.
, Quast C.
and GlÃƒÂ¶ckner F.O.
1,2
Database portal for marine ecological genomics
database
summary
Membranome
Lomize, Andrei; Lomize, Mikhail; Krolicki, Shean; Pogozheva, Irina
A database of single-pass membrane proteins
database
summary
MemMoRF
Hegedus, Tamas; Csizmadia, Georgina; ErdÃ…â€˜s, GÃƒÂ¡bor; Tordai, Hedvig; PadÃƒÂ¡nyi, Rita; Dosztanyi, Zsuzsanna,
Membrane-binding Molecular Recognition Features
database
summary
MemMoRF
Georgina Csizmadia
, GÃƒÂ¡bor ErdÃ…â€˜s
, Hedvig Tordai
, Rita PadÃƒÂ¡nyi
, Silvio Tosatto
, Zsuzsanna DosztÃƒÂ¡nyi
, TamÃƒÂ¡s HegedÃ…Â±s
No description supplied
database
summary
MeMotif
Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, and Michael Schroeder
Linear motifs in alpha-helical transmembrane proteins
database
summary
MEPD: A Medaka gene expression pattern database
Henrich, T.
, Ramialison, M.
, Quiring, R.
, Wittbrodt, B.
, Furutani-Seiki, M.
, Wittbrodt, J.
, Kondoh, H.
Medaka (freshwater fish
Oryzias latipes
) gene expression pattern database
database
summary
MERAV
Shaul, Yoav; Yuan, Bingbing; Thiru, Prathapan; Nutter-Upham, Andy; McCallum, Scott; Lanzkron, Carolyn; Bell, George; Sabatini, David
Metabolic gEne RApid Visualizer
database
summary
MEROPS
Rawlings, Neil; Barrett, Alan; Thomas, Paul; Huang, Xiaosong; Finn, Robert; Bateman, Alex
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source
database
summary
mESAdb
Koray D. Kaya, GÃƒÆ’Ã‚Â¶khan KarakÃƒÆ’Ã‚Â¼lah, Cengiz M. Yak?c?er, Aybar C. Acar, and ÃƒÆ’Ã¢â‚¬â€œzlen Konu
microRNA Expression and Sequence Analysis Database
database
summary
MESPEUS
Hsin, Kun-Yi; Lin, Geng-Yu; Su, Yu-Cheng; Lin Huang, Yen
MESPEUS: a database of metal coordination groups in proteins
database
summary
MeT-DB
Huang, Yufei; Liu, Hui; Wang, Huaizhi; Wei, Zhen; Yao, Songyao; Zhang, Lin; Hua, Gang; Zhang, Shaowu; Gao, Shou-Jiang; Meng, Jia; Chen, Xing
No description supplied
database
summary
MeT-DB
Huang, Yufei; Liu, Hui; Flores, Mario; Meng, Jia; Zhang, Lin; Zhao, Xinyu; Rao, Manjeet; Chen, Yidong
RNA MEthylation by SEquencing databaSe
database
summary
Meta-VR
Nikos Kyrpides; et al.
Meta-Virus Resource (MetaVR): Expanding the Frontiers of Viral Diversity
database
summary
meta.MicrobesOnline
Dylan Chivian
A suite of Web-based comparative genomic tools for metagenome analysis
database
summary
MetaBase
Dan Bolser
Wiki database of biological databases
database
summary
MetabFlow
Lin Tao; et al.
MetabFlow: A comprehensive metabolic map for natural products
database
summary
MetaBioME
Vineet K. Sharma, Naveen Kumar, Tulika Prakash, and Todd D. Taylor
Metagenomic BioMining Engine: homologs of commercially useful enzymes in metagenomic datasets
database
summary
MetaboLights
Christoph Steinbeck
A database for metabolomics experiments and the associated metadata
database
summary
Metabolights
O'Donovan, Claire; Yurekten, Ozgur; Payne, Thomas; Tejera, Noemi; Amaladoss, Felix; Martin, Callum; Williams, Mark,
MetaboLights: open data repository for metabolomics
database
summary
Metabolomics Workbench
Subramaniam, Shankar; Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, Sree; Sumner, Susan
Data repository for metabolomics data and metadata, metabolite standards, protocols, analysis tools, tutorials and training
database
summary
MetaCrop
Biochemical pathways and enzymes in crop plants
database
summary
MetaCyc
Caspi, Ron; Billington, Richard; Fulcher, Carol; Keseler, Ingrid; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Midford, Peter; Ong, Quang; Ong, Wai Kit; Paley, Suzanne; Subhraveti, Pallavi; Karp, Peter
No description supplied
database
summary
Metalog
Michael Kuhn; et al.
Metalog: curated and harmonised contextual data for global metagenomics
database
summary
MetalPDB
Andreini, Claudia; Putignano, Valeria; Rosato, Antonio; Banci, Lucia
No description supplied
database
summary
MetalPDB
Andreini, C.
1,2
, Cavallaro, G.
, Lorenzini, S.
, and Rosato, A.
1,2
Metal-binding sites and their structural environment within macromolecular structures
database
summary
MetaRef
Segata, Nicola; Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis
Metagenomic catalog of clade-specific microbial genes
database
summary
metaRoot
Pavlopoulos; Georgios; et al.
metaRoot: A software for cross-organ and cross-species analysis of plant root systems
database
summary
metaTIGER
Metabolic evolution resource and its application to Plasmodium evolution
database
summary
MetaTraits
Daniel Podlesny; et al.
metaTraits: a large-scale integration of microbial phenotypic trait information
database
summary
MetazExp
Huang, Wen; Liu, Jinding; Yin, Fei; Lang, Kun; Jie, Wencai; Tan, Suxu; Duan, Rongjing; Huang, Shuiqing
Analysis of gene expression and alternative splicing in metazoans
database
summary
MethBank
ngdcbig.ac.cn
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates hig
database
summary
MethBank
Zhang, Mochen; Zong, Wenting; Zou, Dong; Guoliang, Wang; Zhao, Wei; Yang, Fei; Wu, Song; Zhang, Xinran; Guo, Xutong; Ma, Yingke; xiong, zhuang; Zhang, Zhang; Bao, Yi-Ming; Li, Rujiao
MethBank 4.0: an updated database of DNA methylation across a variety of sp
database
summary
MethBank
Zhang, Zhang; Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing
Single-base nucleotide methylomes of gametes and early embryos
database
summary
MethHC
Huang, Hsien-Da; Huang, Hsi-Yuan; Li, Jing,; Tang, Yun; Huang, Yi-Xian; Chen, Yi-Gang; Xie, Yue-Yang; Zhou, Zhe-Yuan; Chen, Xin-Yi; Ding, Si-Yuan; Luo, Meng-Fan; Zhao, Le-Shan; Xu, Jia-Tong; Zhou, Ying; Lin, Yang-Chi-Dung; Hong, Hsiao-Chin; Jin, Chen-Nan;
DNA methylation in human cancer
database
summary
MethMarkerDB
Zhizian Zhu, Qiangwei Zhou, Yuanhi Sun, Fuming Lai, Zhenji Wand, Zhigang Hao, Guolian Li
MethMarkerDB is a comprehensive cancer DNA methylation biomarker database.
database
summary
MethMotif
Benoukraf, Touati; Dyer, Matthew; Lin, Quy Xiao Xuan; Shapoval, Sofiia; Thieffry, Denis
MethMotif.org 2024: A database integrating context-specific transcription factor binding motifs with DNA methylation patterns
database
summary
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles
XuanÃ‚Â Lin, Quy Xiao;Sian, Stephanie;An, Omer;Thieffry, Denis;Jha, Sudhakar;Benoukraf, Touati
No description supplied
database
summary
MethSMRT
Xie, Zhi; Ye, Yohao; Luan, Yizhao; Xiao, Chuanle; Chen, Kaining; Liu, Yizhi
DNA methylation data from single molecule, real-time sequencing
database
summary
MethyCancer
Links between DNA methylation levels and cancer
database
summary
METscout
Gregor Eichele
Spatial organization of metabolic reactions in the mouse
database
summary
metsDB
Liyu Huang
Cancer metastasis with bulk, single-cell and spatial transcriptomics
database
summary
MFunGD
MIPS mouse functional genomics database
database
summary
MG-RAST
Wilke, Andreas; Bischof, Jared; Gerlach, Wolfgang; Glass, Elizabeth; Harrison, Travis; Keegan, Kevin; Paczian, Tobias; Trimble, William; Meyer, Folker
Data portal for the processing, analyzing, sharing and disseminating of metagenomic data sets
database
summary
MGA
Bucher, Philipp; Dreos, RenÃƒÂ©; Ambrosini, Giovanna; Groux, Romain
No description supplied
database
summary
MGAN
Welch, Roy; Pratt-Szeliga, Philip; Skewes, Aaron; Yan, Jinyuan; Welch, Laura
Microbial Genome Annotation Network
database
summary
MGDB
Haiyun Wang; et al.
MGDB: a curated database for molecular glues
database
summary
MGnify
Finn, Robert; Richardson, Lorna; Allen, Ben; Baldi, Germana; Beracochea, Martin; Bileschi, Maxwell L.; Burdett, Tony; Burgin, Josephine; Caballero-PÃ©rez, Juan; Cochrane, Guy; Colwell, Lucy; Curtis, Thomas; Escobar-Zepeda, Alejandra; Gurbich, Tatiana; Kale
MGnify - the microbiome sequence data analysis resource in 2023
database
summary
MGTbind
Jianfeng Pei; et al.
mgtbind: a comprehensive database of molecular glue ternary interactomes
database
summary
MHC Motif Atlas
Tadros, Daniel; Eggenschwiler, Simon; Gfeller, David; Racle, Julien
MHC Binding Specificities and Ligands
database
summary
MHCBN
Bhasin M. and Raghava G.P.S.
A database of MHC binding and non-binding peptides
database
summary
MIBiG
Terlouw, Barbara; Blin, Kai; Navarro-MuÃ±oz, Jorge C.; Avalon, Nicole; Chevrette, Marc; Egbert, Susan; Lee, Sanghoon; Meijer, David; Recchia, Michael J. J.; Reitz, Zachary L.; van Santen, Jeffrey A.; Selem-Mojica, Nelly; TÃ¸rring, Thomas; Zaroubi, Liana; Al
MIBiG 3.0: A community-driven effort to annotate experimentally validated b
database
summary
MicroAgroBiome
Selelem-Mojica; Nelly; et al.
MicroAgroBiome: A toolkit for exploring specialized metabolism and ecological roles of plant-associated microbes
database
summary
MicrobesOnline
Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna L. Dubchak, Eric J. Alm, and Adam P. Arkin
A suite of Web-based tools for comparative genomics
database
summary
MicrobialScope
Shuai Cheng Li; et al.
MicrobialScope: An integrated genomic resource with rich annotations across domains
database
summary
microbiomeDB
Beiting, Daniel; Oliveira, Francislon; Brestelli, John; Cade, Shon; Iodice, John; Fisher, Steve; Aurrecoechea, Cristina; Kissinger, Jessica; Brunk, Brian; Stoeckert, Chris; Fernandes, Gabriel; Roos, David
No description supplied
database
summary
MicrobiomeNet
Jeff Xia
Microbial communities and their metabolism
database
summary
microbioTA
Cheng, Liang; Wang, Ping; Zhang, Sainan; He, Guoyou; Du, Meiyu; Qi, Changlu; Liu, Ruyue; Zhang, Siyuan; Zhang, Xue1
Cancer microbiomes
database
summary
MicroEpitope
Juan Xu
Immune epitopes derived from cancer microbiome
database
summary
MiCroKitS
Huang, Zhengnan; Ma, Lili; Wang, Yongbo; Pan, Zhicheng; Ren, Jian; Liu, Zexian; Xue, Yu
Midbody, Centrosome, Kinetochore and Spindle proteins
database
summary
microRNA.org
microRNA target predictions and expression profiles
database
summary
MicroScope
Claudine Medigue
Microbial Genome Annotation & Analysis Platform
database
summary
MicrosporidiaDB
Functional Genomic Resource for Microsporidia
database
summary
MiMeDB
Wishart, David; Oler, Eponine; Peters, Harrison; Guo, An Chi; Girod, Sagan; Han, Scott; Saha, Sukanta; Liu, Vicki; LeVatte, Marcia; Gautam, Vasuk; Kaddurah-Daouk, Rima; Karu, Naama
Human-microbe interactions and their metabolomes
database
summary
MimoDB
Jian Huang
Mimotope database, active site-mimicking peptides selected from phage-display libraries
database
summary
MINAS
Roland Sigel
Metal Ions in Nucleic AcidS
database
summary
Minimotif miner
Schiller, Martin; Lyon, Ken; Cai, Xingyu; Mamun, Abdullah; Young, Richard; Rajasekaran, Sanguthevar
No description supplied
database
summary
Minimotif Miner
Schiller, Martin; Merlin, Jerlin; Mi, Tian.; Deverasetty, Sandeep; Gryk, Michael; Bill, Travis; Brooks, Andrew; Lee, Logan; Rathnayake, Viraj; Ross, Christian; Sargeant, David; Strong, Christy; Watts, Paula; Rajasekaran, Sanguthevar
Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules
database
summary
MINRbase
Rigoutsos, Isidore; Pliatsika, Venetia; Cherlin, Tess; Loher, Phillipe; Vlantis, Panagiotis I.; Nagarkar, Parth; Nersisyan, Stepan
MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs)
database
summary
MINT
Briganti, Leonardo
; Licata, Luana
; Peluso, Daniele
; Perfetto, Livia
; Iannuccelli, Marta
; Galeota, Eugenia
; Sacco, Francesca
; Palma, Anita
; Nardozza, Aurelio
; Santonico, Elena
; Castagnoli, Luisa
; Cesareni, Gianni
1,2
Molecular INTeraction database
database
summary
MINTbase
Rigoutsos, Isidore; Pliatsika, Venetia; Loher, Phillipe; Magee, Rogan; Telonis, Aristeidis; Shigematsu, Megumi; Kirino, Yohei
MINTbase is a repository that comprises nuclear and mitochondrial tRNA-deri
database
summary
MIPModDB
R. Sankararamakrishnan
Major Intrinsic Protein superfamily Models
database
summary
MIPSPlantsDB
Spannagl, Manuel; Nussbaumer, Thomas; Martis, Mihaela; Rößner, Stephan; Pfeifer, Matthias; Bader, Kai; Sharma, Sapna; Gundlach, Heidrun
MIPS Plants Databases
database
summary
miR2Disease
Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease
database
summary
miRandola
Russo, Francesco; Di Bella, Sebastiano; Vannini, Federica; Berti, Gabriele; Scoyni, Flavia; Cook, Helen; Santos, Alberto; Nigita, Giovanni; Bonnici, Vincenzo; LaganÃƒÂ , Alessandro; GERACI, FILIPPO; Pulvirenti, Alfredo; Giugno, Rosalba; De Masi, Federico; Belling, Kirstine; Jensen, Lars,; Brunak, SÃƒÂ¸ren; Pellegrini, Marco; Ferro, Alfredo
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non
database
summary
miRBase
Kozomara, Ana;Birgaoanu, Maria;Griffiths-Jones, Sam
Database of microRNAs (small noncoding RNAs)
database
summary
miRCarta
Backes, Christina; Fehlmann, Tobias; Kern, Fabian; Kehl, Tim; Lenhof, Hans-Peter; Meese, Eckart; Keller, Andreas
The continuous increase of available biological data as consequence of mode
database
summary
miRDB
Wong, Nathan; Wang, Xiaowei
miRNA target prediction and functional annotation
database
summary
miRDB: an online database for prediction of functional microRNA targets
Chen, Yuhao;Wang, Xiaowei
No description supplied
database
summary
mirDIP
Jurisica, Igor; Tokar, Tomas; Pastrello, Chiara; Rossos, Andrea; Abovsky, Mark; Hauschild, Anne-Christin; Tsay, Mike; Lu, Richard
MicroRNAs are important regulators of gene expression, achieved by binding
database
summary
mirDIP
Hauschild, Anne-Christin; Pastrello, Chiara; Ekaputeri, Gitta Kirana Anindya; Waddell, Dylan Bethune; Abovsky, Mark; Ahmed, Zuhaib; Kotlyar, Max; Lu, Richard; Jurisica, Igor
MirDIP 5.2: tissue context annotation and novel microRNA curation
database
summary
mirDNMR
Jiang, Yi; Li, Zhongshan; Liu, Zhenwei; Chen, Denghui; Wu, Wanying; Du, Yaoqiang; Ji, Liying; Li, Wei.'; Wu, Jinyu
Background de novo mutation rates in human genes
database
summary
miRecords
Tongbin Li
Experimentally validated miRNAs
database
summary
miREX
Wojciech Karlowski
Plant microRNA Expression data
database
summary
miRGator
microRNA target prediction, functional analysis, and gene expression data
database
summary
MirGeneDB
Fromm, Bastian; HÃ¸ye, Eirik; Domanska, Diana; Zhong, Xiangfu; Aparicio-Puerta, Ernesto; Umu, Sinan; Chabot, Peter; Kang, Wenjing; Aslanzadeh, Morteza; Tarbier, Marcel; MÃ¡rmol-SÃ¡nchez, Emilio; Urgese, Gianvito; Johansen, Morten; Hovig, Eivind; Hackenberg,
Animal miRNA complements
database
summary
MirGeneDB 2.0: the metazoan microRNA complement
Fromm, Bastian;Domanska, Diana;HÃƒÂ¸ye, Eirik;Ovchinnikov, Vladimir;Kang, Wenjing;Aparicio-Puerta, Ernesto;Johansen, Morten;Flatmark, Kjersti;Mathelier, Anthony;Hovig, Eivind;Hackenberg, Michael;FriedlÃƒÂ¤nder, Marc R;Peterson, Kevin J
Small non-coding RNAs have gained substantial attention due to their roles
database
summary
MIRIAM Registry
Nick Juty
Minimal Information Required In the Annotation of Models
database
summary
miRNAMap
microRNA precursors and their mapping to targets in vertebrate genomes
database
summary
miRNATissueAtlas
Shusruto Rishik
ncRNA expression across organs and organ systems
database
summary
miRNEST
Makalowska, Izabela; Szczesniak, Michal
microRNAs in animal and plant EST sequences
database
summary
miROrtho
Computational prediction of animal microRNA genes
database
summary
miRPathDB
Keller, Andreas; Backes, Christina; Kehl, Tim; StÃƒÂ¶ckel, Daniel; Fehlmann, Tobias; Schneider, Lara; Meese, Eckart ,; Lenhof, Hans-Peter
Dictionary on miRNAs and their putative target pathways
database
summary
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database
Kehl, Tim;Kern, Fabian;Backes, Christina;Fehlmann, Tobias;StÃƒÂ¶ckel, Daniel;Meese, Eckart;Lenhof, Hans-Peter;Keller, Andreas
No description supplied
database
summary
miRStart
Huang Hsien-Da
miRStart 2.0 is a database designed to provide comprehensive miRNA upstream
database
summary
miRTarBase
Huang Hsien-Da
miRTarBase, the leading repository for miRNA-target interactions (MTIs), ha
database
summary
miRTarBase
Huang, Hsien-Da; Hsu, Sheng-Da; Tseng, Yu-Ting; Shrestha, Sirjana; Lin, Yu-Ling; Khaleel, Anas; Chou, Chih-Hung; Huang, Hsi-Yuan; Lin, Ching-Min; Ho, Shu-Yi; Jian, Ting-Yan; Lin, Feng-Mao; Chang, Tzu-Hao; Weng, Shun-Long; Liao, Kuang-Wen; Liao, I-En; Liu, Chun-Chi
Experimentally validated microRNA-target interactions
database
summary
miRTarBase
Huang, Hsien-Da; Chou, Chih-Hung; Shrestha, Sirjana; Yang, Chi -Dung; Chang, Nai-Wen; Lin, Yu-Ling; Liao, Kuang-Wen; Huang, Wei-Chi; Sun, Ting-Hsuan; Tu, Siang-Jyun; Lee, Wei-Hsiang; Chiew, Men-Yee; Li, Meng-Ju; Wu, Yu-Chun; Huang, Xin-Yi; Ng, Fung Ling; Buddhakosai, Waradee; Huang, Pei-Chun; Lan, Kuan-Chun; Huang, Chia-Yen; Weng, Shun- Long; Cheng, Yeong-Nan; Hsu, Wen-Lian; Tai, Chun-San; Wei, Ting-Yen; Tsai, Tzi-Ren; Huang, Hsin-Tzu; Wang, Chung-Yu; Wu, Yi-Shin; Ho, Shu-Yi; Chen, Pin-Rong; Chuang, Cheng-Hsun; Hsieh, Pei-Jung; Wu, Yi-Shin; Chen, Wen-Liang; Liang, Chao
No description supplied
database
summary
miRTarBase
Huang, Hsien-Da; Huang, Hsi-Yuan; Lin, Yang-Chi-Dung; Cui, Shi-Dong; Huang, Yi-xian; Tang, Yun; Xu, Jiatong; Bao, Jiayang; Li, Yulin; Wen, Jia; Zuo, Hua-Li; Wang, Weijuan; Li, Jing,; Ni, Jie; Ruan, Yini; Li, Liping; Chen, Yidan; Xie, Yue-Yang; Zhu, Zihao;
miRTarBase update 2022: An informative resource for experimentally validate
database
summary
mirTrans
Tang, Rongjun; Hua, Xu; Xu, Xiuxiu; Wang, Zhi; Xu, Qi; Chen, Luxiao; Wingender, Edgar; Li, Jie'; Wang, Jin.
No description supplied
database
summary
MIST
Perrimon, Norbert; Hu, Yanhui; Vinayagam, Arunachalam; Nand, Ankita; Comjean, Aram; Chung, Verena; Hao, Tong; Mohr, Stephanie
Model organism and human databases are rich with information about genetic
database
summary
MiST
Gumerov, Vadim; Ulrich, Luke; Zhulin, Igor
MiST 4.0: a new release of the microbial signal transduction database, now with a metagenomic component
database
summary
MiST 3.0
Vadim M. Gumerov, Davi R. Ortega, Ogun Adebali, Luke E. Ulrich and Igor B. Zhulin
Bacteria and archaea employ dedicated signal transduction systems that modu
database
summary
MITE
Mitja Zdouc; et al.
MITE: The Minimum Information about a Tailoring Enzyme Database for capturing, storing and sharing BGC biosynthetic knowledge
database
summary
miTED
Hatzigeorgiou, Artemis; Kavakiotis, Ioannis; Alexiou, Athanasios; Tastsoglou, Spyros; Vlachos, Ioannis S.
microRNA Tissue Expression Database
database
summary
Mitelman Database
Chromosome Aberrration and Gene Fusions in Cancer
database
summary
MitoAge
Toren, Dmitri; Barzilay, Thomer; Tacutu, Robi; Lehmann, Gilad; Muradian, Khachik; Fraifeld, Vadim
Mitochondrial DNA and longevity
database
summary
MitoBreak - The mitochondrial DNA breakpoints database
Damas, J.
, Carneiro, J.
, Amorim, A.
1, 2
, Pereira, F.
1,3
Mitochondrial DNA breakpoints in human, mouse and rat
database
summary
MitoCarta
Mootha, Vamsi K; Rath, Sneha; Sharma, Rohit; Gupta, Rahul; Ast, Tslil; Chan, Connie; Durham, Timothy; Goodman, Russell; Grabarek, Zenon; Haas, Mary; Hung, Wendy; Joshi, Pallavi; Jourdain, Alexis; Kim, Sharon; Kotrys, Anna; Lam, Stephanie; McCoy, Jason; Me
Mouse and human mitochondrial proteins
database
summary
MitoDrome
DÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢Elia D.
, Catalano D.
, Licciulli F.
, Turi A.
, Tripoli G.
, Porcelli D.
, Saccone C.
2,3
and Caggese C.
Drosophila
nuclear-encoded proteins targeted to the mitochondrion
database
summary
MitoGenesisDB
Jean-Christophe Gelly
1,2,3
, Mickael Orgeurp
, Claude Jacq
and Gae‰lle Lelandais
1,2,3
Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis
database
summary
MitoMiner
Alan Robinson
Mitochondrial proteomics data
database
summary
MitoProteome
Mitochondrial protein sequences encoded by mitochondrial and nuclear genes
database
summary
MMCD
A resource for metabolomics research based on nuclear magnetic resonance spectroscopy and mass spectrometry.
database
summary
MMDB
Madej, Tom; Addess, Kenneth; Fong, Jessica; Geer, Lewis; Geer, Renata; Lanczycki, Christopher; Liu, Chunlei; Lu, Shennan; Marchler-Bauer, Aron; Panchenko, Anna; Chen, Jie; Thiessen, Paul; Wang, Yanli; Zhang, Dachuan; Bryant, Steve
All experimentally-determined 3D structures, linked to NCBI Entrez
database
summary
mMGE
Chen, Weihua; Lai, Senying; Jia, Longhao; Subramanian, Balakrishnan; Pan, Shaojun; Zhang, Jinglong; Dong, Yanqi; Zhao, Xing-Ming
Human metagenomic extrachromosomal mobile genetic elements
database
summary
MMMDB
Masahiro Sugimoto
Mouse Multiple Tissue Metabolomics Database
database
summary
MMP
Willassen, Nils Peder; Klemetsen, Terje; Raknes, Inge Alexander; Fu, Juan; Agafonov, Aleksander.; Balasundaram, Sudhagar; Tartari, Giacomo; Robertsen, Espen
No description supplied
database
summary
MMsINC
Database of commercially-available compounds for virtual screening and chemoinformatics
database
summary
MNDR
Wang, Dong; Ning, Lin; Cui, Tianyu; Zheng, Boyang; Wang, Nuo; Luo, Jiaxin; Yang, Beilei; Du, Mengze; Dou, Yiying
No description supplied
database
summary
MNXref/MetaNetX
Pagni, Marco; Moretti, SÃƒÂ©bastien; Tran, Van Du; Mehl, Florence; Ibberson, Mark
Genome-scale metabolic networks
database
summary
MobiDB
Tosatto, Silvio; Piovesan, Damiano; Necci, Marco; escobedo, nahuel; Monzon, Alexander; Hatos, Andras; MiÃ„\x8DetiÃ„â€¡, Ivan; Quaglia, Federica; Paladin, Lisanna; Ramasamy, Pathmanaban; Dosztanyi, Zsuzsanna,; Vranken, Wim; Davey, Norman; Parisi, Gustavo; Fuxreiter
Database of protein disorder and mobility annotations.
database
summary
MobiDB
Tosatto, Silvio; Potenza, Emilio; Di Domenico, Tomas; Walsh, Ian
Intrinsically disordered and mobile proteins
database
summary
MobiDB
Tosatto, Silvio; Piovesan, Damiano; Del Conte, Alessio; Clementel, Damiano; Monzon, Alexander; Bevilacqua, Martina; Aspromonte, Maria Cristina; Iserte, Javier; Orti, Fernando; Marino-Buslje, Cristina
MobiDB: ten years of intrinsically disordered proteins
database
summary
ModBase
Pieper, U., Eswar, N., Stuart, A.C., Braberg, H., Madhusudhan, M.S., Davis, F., Rossi, A., Marti-Renom, M.A., Sali, A.
Annotated comparative protein structure models
database
summary
ModelSEED
Samuel M D Seaver
, Filipe Liu
, Qizhi Zhang
, James Jeffryes
, JosÃƒÂ© P Faria
, Janaka N Edirisinghe
, Michael Mundy
, Nicholas Chia
, Elad Noor
, Moritz E Beber
, Aaron A Best
, Matthew DeJongh
, Jeffrey A Kimbrel
, Patrik DÃ¢â‚¬â„¢haeseleer
, Sean R McCorkle
, Jay R Bolton
, Erik Pearson
, Shane Canon
, Elisha M Wood-Charlson
, Robert W Cottingham
10
, Adam P Arkin
, Christopher S Henry
The ModelSEED (https://modelseed.org) biochemistry database serves as the f
database
summary
modMine
Sergio Contrino
Mining of modENCODE data
database
summary
MODOMICS
Czerwoniec, A.
, Dunin-Horkawicz, S.
, Purta, E.
3,4
, Kaminska, K.H.
, Kasprzak, J.M.
, Bujnicki, J.M.
1,3
, Grosjean, H.
, and Rother, K.
A database of RNA modification pathways
database
summary
MODOMICS
Bujnicki, Janusz M.; Boccaletto, Pietro; Machnicka, Magdalena; Purta, Elzbieta; Piatkowski, Pawel; Baginski, Blazej; Wirecki, Tomasz; de Crecy-Lagard, Valerie; Ross, Robert; Limbach, Patrick; Kotter, Annika; Helm, Mark
No description supplied
database
summary
MODOMICS
Bujnicki, Janusz; Cappannini, Andrea; Ray, Angana; Purta, Elzbieta; Mukherjee, Sunandan; Boccaletto, Pietro; Moafinejad, Seyed Naeim; Lechner, Antony; Barchet, Charles; Klaholz, Bruno; Stefaniak, Filip
MODOMICS: a database of RNA modifications and related information. 2023 update
database
summary
MODOMICS
Bujnicki, Janusz; Boccaletto, Pietro; Stefaniak, Filip; Ray, Angana; Cappannini, Andrea; Mukherjee, Sunandan; Purta, Elzbieta; Durawa, Malgorzata; Shirvanizadeh, Niloofar; Destefanis, Eliana; Groza, Paula; AvÅŸar, GÃ¼lben; Romitelli, Antonia; Pir, Pnar; Das
RNA modification pathways
database
summary
MoKCa
Mutations of Kinases in Cancer
database
summary
MolBiC
Feng Zhu
Molecular Bioactivities in Cells
database
summary
MolGlueDB
Wang, Xiao; Zhuang, Zhiyao; Zhang, Chengwei; Zhang, Bowen; Zhan, Wei; Wang, Yifan; Liu, Zhaojuan; Yuan, Shanwen; Niu, Wenjia; He, Qi; Tian, Yanqing; Xu, Ximing; Fang, Senbiao; Qin, Chong
A free and open-access online database dedicated to the collection and integration of molecular glue compound information.
database
summary
MolliGen
Genomic data on mollicutes
database
summary
MolluscDB
Wang, Shi; Liu, Fuyun; Li, Yuli; Yu, Hongwei; Zhang, Lingling; Hu, Jingjie; Bao, Zhenmin
Comparative genomics of molluscs
database
summary
MolMovDB - Database of Macromolecular Movements
Descriptions of protein and macromolecular motions, including movies
database
summary
Monarch Initiative
Munoz-Torres, Monica (proxy) (contact); Putman, Tim; Schaper, Kevin; Matentzoglu, Nicolas; Rubinetti, Vincent; Alquaddoomi, Faisal; Cox, Corey; Caufiled, Harry; Elsarboukh, Glass; Gehrke, Sarah; Hegde, Harshad; Reese, Justin; Braun, Ian; Bruskiewich, Richard; Cappelletti, Luca; Carbon, Seth; Caron, Anita; Chan, Lauren; Chute, Christopher; Cortes, Katherina; De Souza, VinÃcius; Fontana, Tommaso; Harris, Nomi; Hartley, Emily; Hurwitz, Eric; Jacobsen, Julius; Krishnamurthy, Madan; Laraway, Bryan; McLaughlin, James; McMurry, Julie; Moxon, Sierra; Mullen, Kathleen; Oneil, Shawn; Shefchek, Kent; Stefancsik, Ray; Toro, Sabrina; Vasilevsky, Nicole; Walls, Ramona; Whetzel, Trish; Osumi-Sutherland, David; Smedley, Damian; Robinson, Peter; Mungall, Christopher; Haendel, Melissa
Human disease-related phenotypes in model organisms
database
summary
MonarchBase
Zhan, S.
and Reppert, S.M.
Genome biology of the monarch butterfly
Danaus plexippus
database
summary
MoonProt
Chang Chen
1,2
, Haipeng Liu
, Shadi Zabad
, Nina Rivera
, Emily Rowin
, Maheen Hassan
, Stephanie M. Gomez De Jesus
, Paola S. LlinÃƒÂ¡s Santos
, Karyna Kravchenko
, Mariia Mikhova
, Sophia Ketterer
, Annabel Shen
, Sophia Shen
, Erin Navas
10
, Bryan Horan
10
, Jaak Raudsepp
and Constance Jeffery
1,5
MoonProt 3.0 is an updated open-access database storing expert-curated anno
database
summary
MoonProt
Mani, Mathew; Chen, Chang; Amblee, Vaishak; Liu, Haipeng; Mathur, Tanu; Zwicke, Grant; Zabad, Shadi; Patel, Bansi; Thakkar, Jagravi; Jeffery, Constance
Moonlighting proteins
database
summary
MOsDB
Karlowski W.
, Schoof H.
2,3
, Spannagl M.
2,3
, Yang L.
and Mayer K.F.X.
MIPS
Oryza sativa
database
database
summary
mOTUs-db
Shinichi Sunagawa
Prokaryotic (metagenome-assembled) genomes
database
summary
Mouse Genome Database
Blake, Judith; Baldarelli, Richard; Kadin, James; Richardson, Joel; Smith, Cynthia; Bult, Carol; Mouse Genome Database Group, MGD
No description supplied
database
summary
Mouse Phenome Database
Grubb, Stephen; Bult, Carol; Bogue, Molly
Phenotypic and genotypic data from inbred strains of mice
database
summary
Mouse Phenome Database
Bogue, Molly; Grubb, Stephen; Walton, David; Philip, Vivek; Kolishovski, Georgi; Stearns, Tim; Dunn, Matthew H; Skelly, Daniel A; Kadakkuzha, Beena; TeHennepe, Gregg; Kunde-Ramamoorthy, Govind; Chesler, Elissa
The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely used
database
summary
Mousebook
Andrew Blake, Karen Pickford, Simon Greenaway, Steve Thomas, Amanda Pickard, Christine M. Williamson, Niels C. Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
Mutant mouse lines held at MRC Harwell
database
summary
MouseIndelDB
Mouse Indel Polymorphism Database
database
summary
MouseNet
Lee, Insuk; Kim, Eiru; Hwang, Sohyun; Kim, Hyojin; Shim, Hongsuk; Kang, Byunghee; Yang, Sunmo; Shim, Jae Ho; Shin, Seung Yeon; Marcotte, Edward
Functional network of mouse genes
database
summary
MouseOMICS
Yujing Ying; et al.
MouseOMICS: a multi-omics database for mouse biological study
database
summary
MP:PD
Hildebrand, Peter; Rose, Alexander S; Theune, Dominic; Goede, Andrean
Membrane Proteins: Packing Densities, packing defects and internal water molecules
database
summary
MPD
Bogue, Molly; Ball, Robyn; Philip, Vivek; Walton, David; Dunn, Matthew H; Kolishovski, Georgi; Lamoureux, Anna; Liang, Hongping; Emerson, Jake; Stearns, Tim; He, Hao; Mukherjee, Gaurab.; Bluis, John; Desai, Sejal; Sundberg, Beth; Kadakkuzha, Beena; Kunde-
Mouse Phenome Database: Towards a more FAIR-compliant and TRUST-worthy data
database
summary
MPDB - Molecular Probe Database
Marra, D., Romano, P.
Information on synthetic oligonucleotides proven useful as primers or probes
database
summary
MPIM - Mitochondrial Protein Import Machinery
Mitochondrial protein import machinery of plants
database
summary
MRPrimerV
Kim, Min-Soo; Kim, Hyerin; Kang, Nana; An, KyuHyeon; Kim, Doyun; Koo, JaeHyung
PCR primer pairs for detecting RNA virus-mediated infectious diseases
database
summary
MSDB: a comprehensive, annotated database of microsatellites
Avvaru, Akshay Kumar;Sharma, Deepak;Verma, Archana;Mishra, Rakesh K;Sowpati, Divya Tej
No description supplied
database
summary
MSDD
Li, Xia; Yue, Ming; Zhou, Dianshuang; Zhi, Hui'; Wang, Peng,.; Zhang, Yan *; Gao, Yue'; Guo, Maoni; Li, Xin,; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei
No description supplied
database
summary
mSignatureDB
Tang, Petrus; Huang, Po-Jung; Chiu, Ling-Ya; Lee, Chi -Ching; Yeh, Yuan-Ming; Huang, Kuo-Yang; Chiu, Cheng-Hsun
Cancer is a genetic disease caused by somatic mutations; however, the under
database
summary
msRepDB
Gao, Xin; Liao, Xingyu; Hu, Kang; Salhi, Adil; Zou, You; Wang, Jianxin,
multi-species Repeat DataBase
database
summary
MSY Breakpoint Mapper
Sequence-tagged sites in the human Y chromosome
database
summary
MtbRegList
Jacques P.E.
1,2
, Gervais A.L.
1,2
, Cantin M.
, Lucier J.F.
, Dallaire G.
, Drouin G.
, Gaudreau L.
, Goulet J.
and Brzezinski R.
Gene expression in
Mycobacterium tuberculosis
database
summary
MUGEN Mouse Database
Murine models of immune processes and immunological diseases14
database
summary
MulPSSM
Ramakrishnan G., Mohanty S., Krishnadev O. and Srinivasan N.
A searchable database of multiple position specific scoring matrices of protein domain families.
database
summary
MultifacetedProtDB
Martelli, Pier Luigi; Bertolini, Elisa; Babbi, Giulia; Savojardo, Castrense; Casadio, Rita
MultifacetedProtDB: a database of human proteins with multiple functions
database
summary
MultiTaskDB
Querol, Enrique; HernÃƒÂ¡ndez, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; PiÃƒÂ±ol, Jaume; Mozo-Villarias, Angel; Cedano, Juan
Moonlighting Proteins DataBase
database
summary
MultitaskProtDB-II
Querol, Enrique; Franco, LuÃƒÂs; HernÃƒÂ¡ndez, Sergio; Calvo, Alejandra; Seveni, MarÃƒÂaÃƒ\x81ngela; Ferragut, Gabriela; Perez-Pons, JosepAntoni; PiÃƒÂ±ol, Jaume; Pich, Oscar; Mozo-Villarias, Angel; Amela, Isaac; Cedano, Juan
No description supplied
database
summary
MutationAligner
Miller, Martin; Gauthier, Nicholas; Reznik, Ed; Gao, JianJiong; Sumer, Selcuk; Schultz, Nikolaus; Sander, Chris
Somatic mutation hotspots in protein domains in cancer
database
summary
MutDB
Predicted biochemical effects of human genetic variation: maping of SNPs on protein sequence and structure
database
summary
mutLBSgeneDB
Zhao, Zhongming; Kim, Pora; Zhao, Junfei; Lu, Pinyi
Mutations in Ligand Binding Sites gene DataBase
database
summary
MutSpliceDB
Alida Palmisano; Dmitriy Sonkin
MutSpliceDB: A database of splice sites variants with RNA-seq based evidenc
database
summary
MVIP
Zhou, Yu; Tang, Zhidong; Fan, Weiliang; Li, Qiming; Wen, Miaomiao; Li, Xingqiao; Wang, Junhao
Multi-omics Portal of Viral Infection
database
summary
MvirDB
Zhou C.E.Z., Smith J., Lam M.W., Zemla A.T., Dyer M. and Slezak T.
Protein toxins, virulence factors, and antibiotic resistance genes
database
summary
mVOC
Preissner, Robert; Lemfack, Chantal; Gohlke, BjÃƒÂ¶rn; Toguem, Serge; Preissner, Saskia; Piechulla, Birgit
No description supplied
database
summary
mVOC
Piechulla, Birgit; Lemfack, Chantal; nickel, janette; Dunkel, Mathias; Preissner, Robert
Microbial Volatile Organic Compounds
database
summary
MVP
Chen, Weihua; Gao, Na L; Zhang, Chengwei; Zhang, Zhanbing; Hu, Songnian; Lercher, Martin; Zhao, Xing-Ming; Bork, Peer; Liu, Zhi
Phages invade microbes, accomplish host lysis and are of vital importance i
database
summary
MycoCosm
Grigoriev, Igor; Nikitin, Roman; Harids, Sajeet; Kuo, Alan; Ohm, Robin; Otillar, Robert; Riley, Robert; Salamov, Asaf; Zhao, Xueling; Korzeniewski, Frank; Smirnova, Tatyana; Nordberg, Henrik; Dubchak, Inna; Shabalov, Igor
Genomics resources of the DOE Joint Genome Institute
database
summary
NACDDB
Wien, Frank; Cappannini, Andrea; Mosca, Kevin; Mukherjee, Sunandan; Moafinejad, Seyed Naeim; Sinden, Richard; Arluison, Veronique,; Bujnicki, Janusz M.
Nucleic Acid Circular Dichroism Database
database
summary
NAIRDB
Janusz Bujnicki
Nucleic Acid InfraRed Data Bank
database
summary
NAKB
Lawson, Catherine; Berman, Helen; Chen, Li; Vallat, Brinda; Zirbel, Craig
The Nucleic Acid Knowledgebase: A New Portal for 3D Structural Information about Nucleic Acids
database
summary
Nanobase.org
Sulc, Petr; Poppleton, Erik; Mallya, Aatmik; Dey, Swarup; Joseph, Joel
DNA, RNA or protein-DNA/RNA hybrid nanostructures
database
summary
NAPP
Daniel Gautheret
Nucleic Acid Phylogenetic Profile database
database
summary
NapRNADB
Jiajia Xuan; Junfeng Xia; et al.
NapRNADB: a multi-species repository and analytical platform for napRNA
database
summary
Narcisse
Conserved syntenies for various animal, plant and bacterial genomes
database
summary
NASA OSDR
Ryan Scott
NASA Open Science Data Repository
database
summary
NASCarrays (obsolete)
Nottingham Arabidopsis Stock Centre microarray database
database
summary
National Genomics Data Center
Xue, Yongbiao; Bao, Yi-Ming; Zhang, Zhang; Zhao, Wen-Ming; Xiao, Jingfa; He, Shunmin; Zhang, Guo-Qing; Li, Yixue; Zhao, Guoping; Chen, Runsheng
Database Resources of the National Genomics Data Center
database
summary
National Genomics Data Center
Zhang Zhang
Database Resources of the National Genomics Data Center
database
summary
NATsDB
Yong Zhang
, Jiongtang Li
, Lei Kong
, Ge Gao
, Qing-Rong Liu
and Liping Wei
Natural Antisense Transcripts DataBase
database
summary
NBDB
Berezovsky, Igor; Zheng, Zejun; Goncearenco, Alexander
Nucleotide Binding DataBase: nucleotide binding signatures
database
summary
NCATS Inxight: Drugs
Southall, Noel; Siramshetty, Vishal; Grishagin, Ivan; Nguyen, Dac-Trung; Peryea, Tyler; Skovpen, Yulia; Stroganov, Oleg; Katzel, Daniel; Sheils, Timothy; Jadhav, Ajit; MathÃ©, Ewy
Drugs, their properties and regulation
database
summary
NCBI BioSample/BioProject
Ilene Mizrachi
BioProject and BioSample databases at NCBI
database
summary
NCBI BioSystems
Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, and Stephen H. Bryant
Biological pathways with associated literature, molecular, sequence, and chemical data
database
summary
NCBI Bookshelf
Marilu Hoeppner
No description supplied
database
summary
NCBI Protein database
All protein sequences: translated from GenBank and imported from other protein databases
database
summary
NCBI Taxonomy
Eric Cox
The NCBI Taxonomy Database includes names and classifications for all of th
database
summary
NCBI Viral genomes
Viral genome resource at NCBI
database
summary
NCIR - Non-Canonical Interactions in RNA
Nagaswamy, U., Huang, H-C., Larios-Sanz, M., Wang, J., Zhao, Q., Fox, G.E.
Non-standard base-base interactions in known RNA structures
database
summary
ncPlantDB
Ming Chen
Plant ncRNAs and potential encoded peptides
database
summary
ncRNADrug
Xinyu Cao, Xu Zhou, Fei Hou, Yu-e Huang, Mengqin Yuan, Min Long, Sina Chen, Wanyue Lei, Jicun Zhu, Jiahao Chen, Tao Zhang, An-Yuan Guo, and Wei Jiang
ncRNADrug: a database for validated and predicted ncRNAs associated with drug resistance and targeted by drugs
database
summary
ncRNAs database
Szymanski, M.
, Erdmann, V.A.
, Barciszewski, J.
Noncoding RNAs with regulatory functions
database
summary
NDB
Berman, Helen; Coimbatore Narayanan, Buvna; Westbrook, John; Ghosh, Saheli; Petrov, Anton I.; Sweeney, Blake; Zirbel, Craig; Leontis, Neocles
Nucleic acid-containing structures
database
summary
NECTAR
Gong, Sungsam; Ware, James; Walsh, Roddy; Cook, Stuart
Disease-related non-synonymous mutations
database
summary
Negatome
Frishman, Dmitrij; Blohm, Philipp; Frishman, Goar; Smialowski, Pawel; Goebels, Florian; Wachinger, Benedikt; Ruepp, Andreas
A database of non-interacting proteins
database
summary
NEIBank
Wistow G.
, Peterson K.
, Gao J.
, Buchoff P.
, Hauser M.A.
, Bowes Rickman C.
and Hoover D.
EyeSAGE, EyeBrowse and Eye Disease Gene Databases
database
summary
Nematodes.org
Sujai Kumar
Wiki for coordinating nematode sequencing projects
database
summary
NEMBASE
Nematode sequence and functional data database
database
summary
NEMO Archive
Ament, Seth; Adkins, Ricky; Carter, Robert; Chrysostomou, Elena; Colantuoni, Carlo; Crabtree, Jonathan; Creasy, Heather; Degatano, Kylee; Felix, Victor; Gandt, Peter; Garden, Gwenn; Giglio, Michelle; Herb, Brian; Khajouei, Farzaneh; Kiernan, Elizabeth; Mc
Neuroscience Multi-Omic Archive
database
summary
NESbase
la Cour, T.
, Gupta, R.
, Rapacki, K.
, Skriver, K.
, Poulsen, F. M.
, Brunak, S.
Nuclear export signals
database
summary
NetAffx
Public Affymetrix probesets and annotations
database
summary
Network of Cancer Genes
An, O.
, Pendino, V.
, D'Antonio, M.
, Ratti, E.
, Gentilini, M.
, Ciccarelli, F.
1,2
Network properties of cancer genes
database
summary
Network Portal
Baliga, Nitin; Turkarslan, Serdar; Wurtmann, Elisabeth; Wu, Wei-Ju; Jiang, Ning; Bare, J; Foley, Karen; Novichkov, Pavel
A database of gene transcription regulatory networks
database
summary
NetworKIN
Network approach to human protein kinases and their substrate proteins
database
summary
NetwoRx
Kristen Fortney
Chemogenomic experiments in yeast: connection of drug response to biological pathways, phenotypes, and networks
database
summary
Newt-omics
Thilo Borchardt
Data on red spotted newt Notophthalmus viridescens
database
summary
NeXO
Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael; Yu, Michael; Pratt, Dexter; Demchak, Barry; Ideker, Trey
Network Extracted gene Ontology database
database
summary
neXtProt
Zahn-Zabal, Monique; Michel, Pierre-AndrÃƒÂ©; Gateau, Alain; Nikitin, FrÃƒÂ©dÃƒÂ©ric; Schaeffer, Mathieu; Audot, Estelle; Gaudet, Pascale; Duek, Paula D; Teixeira, Daniel; Rech de Laval, Valentine; Samarasinghe, Kasun; Bairoch, Amos; Lane, Lydie
Knowledge platform centered on human proteins
database
summary
NGSmethDB
Oliver, Jose; Geisen, Stefanie; Barturen, Guillermo; Alganza, Ãƒ\x81ngel; Hackenberg, Michael
Next-generation sequencing single-cytosine-resolution DNA methylation data
database
summary
NHPRTR
Peng, Xinxia; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Nishida, Andrew; Pipes, Lenore; Bozinoski, Marjan; Thomas, Matthew; Kelly, Sara; Weiss, Jeffrey; Raveendran, Muthuswamy; Muzny, Donna; Gibbs, Richard; Rogers, Jeffrey; Schroth, Gary; Katze, Michael; Mason, Christopher
Nonhuman Primate Reference Transcriptome Resource
database
summary
NIAS
Masaru Takeya
, Fukuhiro Yamasaki
, Shihomi Uzuhashi
, Takayuki Aoki
Hiroyuki Sawada
, Toshirou Nagai
, Keisuke Tomioka
, Norihiko Tomooka
,Toyozo Sato
and Makoto Kawase
Databases for genetic resources and plant disease information
database
summary
NIH Genetic Testing Registry
Wendy Rubinstein
No description supplied
database
summary
NLRscape
Petrescu, Andrei; Martin, Eliza; Ion, Catalin F.; Ifrimescu, Florin; Spiridon, Laurentiu; Bakker, Jaap; Goverse, Aska
Plant Nod-like receptors
database
summary
NLSdb
Nair, Rajesh
, Carter, Phil
, Rost, Burkhard
Nuclear localization signals
database
summary
NLSdb
Bernhofer, Michael; Goldberg, Tatyana; Wolf, Silvana; Ahmed, Mohamed; Zaugg, Julian; Boden, Mikael; Rost, Burkhard
No description supplied
database
summary
NMDC Data Portal
Eloe-Fadrosh, Emiley; Ahmed, Faiza; Anubhav, Anubhav; Babinski, Michal; Baumes, Jeffrey; Beezley, Jonathan; Borkum, Mark; Bramer, Lisa; Canon, Shane; Christianson, Danielle; Corilo, Yuri; Davenport, Karen; Davis, Brandon; Drake, Meghan; Duncan, William; F
Multi-omics microbiome data
database
summary
NMPdb - Nuclear matrix associated proteins database
Nuclear matrix associated proteins database
database
summary
NMPFamsDB
Pavlopoulos, Georgios; Baltoumas, Fotis; Karatzas, Evangelos; Liu, Sirui; Ovchinikov, Sergey; Sofianatos, Yorgos; Chen, I-Min; Kyrpides, Nikos
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes
database
summary
NNDB
Douglas H. Turner and David H. Mathews
Nearest Neighbor parameters for predicting RNA folding
database
summary
non-B DB
Regina Z. Cer, Kevin H. Bruce, Uma S. Mudunuri, Ming Yi, Natalia Volfovsky, Brian T. Luke, Albino Bacolla, Jack R. Collins, and Robert M. Stephens
non-B DNA forming motifs in mammalian genomes
database
summary
NONCODE
Zhao, Yi; Zhao, LianHe; Wang, Jiajia; Li, Yanyan .; Song, Tingrui; Wu, Yang; Fang, ShuangSang; Bu, Dechao; Li, Hui; Sun, Liang.; Pei, Dong; Zheng, Yu; Huang, Jianqin; Chen, Runsheng; He, Shunmin
A database of noncoding RNAs
database
summary
NONCODEv5
Zhao, Yi; fang, shuangsang; Zhang, Lili; Guo, Jin-Cheng; Niu, Yiwei; Wu, Yang; Zhao, LianHe; Li, XiYuan; Li, Hui; Teng, XveYi; Sun, XianHui; Sun, Liang; Chen, Runsheng
No description supplied
database
summary
NOPdb: Nucleolar Proteome Database
Leung A.K.
, Trinkle-Mulcahy L
. and Lamond, A.I.
Nucleolar proteome database
database
summary
NORINE
A database of nonribosomal peptides
database
summary
NP-MRD
Wishart, David; Sayeeda, Zinat; Budinsky, Zachary; Guo, An Chi; Lee, Brian; Berjanskii, Mark; Rout, Manoj; Peters, Harrison; Dizon, Raynard; Mah, Robert; Torres-Calzada, Claudia; Hiebert-Giesbrecht, Mickel; Varshavi, Dorna; Varshavi, Dorsa; Oler, Eponine;
Natural Products Magnetic Resonance Database
database
summary
NPACT
Subhash Agarwal
Naturally occuring Plant based Anticancerous Compound Targets
database
summary
NPASS
Zhi Xie; et al.
NPASS database update 2026: comprehensive quantitative composition, biological activity and target information for natural products
database
summary
NPASS
Zhao, Hui; Chen, Yu Zong; Yang, Yuan; Wang, Shuaiqi; Yang, Xue; Zhou, Kaicheng; Zhang, Xuyao; Hou, Dongyue; Li, Xingxiu; Lin, Hanbo; Fan, Jiajun; Tan, Ying'; Wang, Shanshan; Zhuoma, Dongzhi; Zhang, Fengying; Zeng, Xian; Ju, Dianwen; Chu, Xinyi
NPASS database update 2023: quantitative natural product activity and speci
database
summary
NPASS
Chen, Yu-Zong; Zeng, Xian; Zhang, Peng,,; He, Wei Dong; Qin, Chu; Chen, Shangying; Tao, Lin; Wang, Yali; Tan, Ying; Gao, Dan; Wang, Bo Hua; Chen, Zhe; Chen, Wei Ping; Jiang, Yuyang
No description supplied
database
summary
NPAtlas
Linington, Roger; van Santen, Jeffrey; Poynton, Ella; Iskakova, Dasha; McMann, Emily; Alsup, Tyler; Clark, Trevor; Fergusson, Claire; Fewer, David; Hughes, Alison; McCadden, Caitlin; Parra Villalobos, Jonathan; Soldatou, Sylvia; Rudolf, Jeffrey; Janssen,
Natural Products Atlas
database
summary
NPCDR
Zhou, Ying; et al.
NPCDR: an integrated database for Natural Product-induced Cell Death Responses
database
summary
NPCDR
Quan Gao , Xinyuan Yu , Kaixuan Liu , Zhiyu Zhu , Mengting Chen , Xiaohong Zhao , Zehua Liao , Lihui Xu , Ying Zhou , Feng Zhu , Xinbing Sui
NPCDR: an integrated database for Natural Product-induced Cell Death Responses
database
summary
NPD - Nuclear Protein Database
Dellaire, G.
, Farrall, R.
, Bickmore, W.A.
Proteins localized in the nucleus
database
summary
NPIDB (Nucleic acids ÃƒÂ¢Ã¢â€šÂ¬Ã¢â‚¬Å“ Protein Interaction DataBase)
Sergei Spirin
Database of structures of nucleic acid - protein complexes
database
summary
NPInter
Wu T.
1,3
, Wang J.
1,3
, Liu C.
2,3
, Zhang Y.
1,3
, Shi B.
1,3
, Zhu X.
1,3
, Zhang Z.
1,3
, SkogerbÃƒÆ’Ã‹Å“ G.
, Chen L.
2,3
, Lu H.
2,3
, Zhao Y.
and Chen R.
1,2
Noncoding RNA-protein interactions
database
summary
NPInter
Zheng, Yu; Luo, Huaxia,; Teng, XueYi; Hao, Xinpei; Yan, Xiaoyu; Tang, Yiheng; Zhang, Wanyu; Wang, Yuanxin; Zhang, Peng; Li, Yanyan; Chen, Runsheng; He, Shunmin
NPInter v5.0: ncRNA interaction database in new era
database
summary
NPInter v4.0: an integrated database of ncRNA interactions
Teng, Xueyi;Chen, Xiaomin;Xue, Hua;Tang, Yiheng;Zhang, Peng;Kang, Quan;Hao, Yajing;Chen, Runsheng;Zhao, Yi;He, Shunmin
No description supplied
database
summary
NPRD - Nucleosome Positioning Region Database
Nucleosome positioning region database
database
summary
NRED
Noncoding RNA Expression Database
database
summary
NRG-CING
Jurgen Doreleijers
Validated NMR structures of proteins and nucleic acid
database
summary
NRichD
Richa Mudgal
, Sankaran, Sandhya
, Gayatri Kumar
, Ramanathan Sowdhamini
, Nagasuma R Chandra
and Narayanaswamy Srinivasan
Sequence databases enriched with computationally designed protein-like sequences
database
summary
NSDNA
Wang, Lihua; Wang, Jianjian; Cao, Yuze; Zhang, Huixue; Wang, Tianfeng; Tian, Qinghua; Lu, Xiaoyu; Lu, Xiaoyan; Kong, Xiaotong; Liu, Zhaojun; Wang, Ning; Zhang, Shuai; Ma, Heping; Ning, Shangwei
Nervous System Disease NcRNAome Atlas
database
summary
NucleaRDB
Vroling, Bas; Thorne, David; McDermott, Philip; Joosten, Henk-Jan; Attwood, Teresa; Pettifer, Steve; Vriend, Gert
Nuclear receptor superfamily
database
summary
Nucleome Data Bank
Onuchic, JosÃƒÂ©; CONTESSOTO, VINICIUS; Cheng, Ryan; Hajitaheri, Arya; Rojas, Esteban; Mello, Matheus; Aiden, Erez; Wolynes, Peter; Di Pierro, Michele
3D genome structures and simulations
database
summary
NucMap: a database of genome-wide nucleosome positioning map across species
Zhao, Yongbing;Wang, Jinyue;Liang, Fang;Liu, Yanxia;Wang, Qi;Zhang, Hao;Jiang, Meiye;Zhang, Zhewen;Zhao, Wenming;Bao, Yiming;Zhang, Zhang;Wu, Jiayan;Asmann, Yan W;Li, Rujiao;Xiao, Jingfa
No description supplied
database
summary
NutriChem
Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene
Nutritional and medicinal value of plant-based foods
database
summary
O-GlcNAc Database
Stephanie Olivier-Van Stichelen, Florian Malard, Eugenia Wulff, Rex Berendt, Laura Danner, Logan Massman, Lazaro Vergara, Uchechi Jennifer Nworah, Kaeley Kroenke, Yiwen Cui, Roel Gonzalez, Sarai Luna, Lilyanna Massman, Adam Knier, Candice Tacconi
The O-GlcNAc database is a curated repository of O-GlcNAcylated proteins, m
database
summary
O-GLYCBASE
Julenius, K., Rapacki, K., Brunak, S., Gupta, R.
O- and C-linked glycosylation sites in proteins
database
summary
Ocean-M
Wang, Shi; et al.
Ocean-M: an integrated global-scale multi-omics database for marine microbial research
database
summary
ODB - Operon database
Okuda S.
, Katayama T.
, Kawashima S.
, Goto S.
and Kanehisa M.
Operon database
database
summary
OED
Enze Huang; et al.
Open Enzyme Database: A Community-Wide Repository for Sharing Enzyme Kinetic Data
database
summary
OGEE
Chen, Weihua; Gurumayum, Sanathoi; Jiang, Puzi; Hao, Xiaowen; Campos, Tulio; Young, Neil; Korhonen, Pasi; Gasser, Robin; Bork, Peer; Zhao, Xing-Ming; He, Lijie
Online GEne Essentiality database
database
summary
OGRDB
William Lees
, Christian E. Busse
, Martin Corcoran
, Mats Ohlin
, Cathrine Scheepers
5,6
, Frederick A. Matsen, IV
, Gur Yaari
, Corey T. Watson
, Andrew Collins
10
, and Adrian J. Shepherd
OGRDB is a curated database of immunoglobulin and T cell receptor sequences
database
summary
OGRe - Organellar Genome Retrieval
Tang B., Xu W., Jameson D., Higgs P.
Mitochondrial genome sequences, gene orders and codon usage tables
database
summary
OikoBase
John Manak
A curated genome expression database of Oikopleura dioica
database
summary
OKCAM - now available at RhesusBase
Ontology-based Knowledgebase for Cell Adhesion Molecules
database
summary
OlfactionBase
Varadwaj, Pritish; Sharma, Anju; Saha, Bishal; Kumar, Rajnish
Odors, Odorants and Olfactory Receptors
database
summary
Olfactory Receptor Database
Sequences for lfactory receptor-like molecules
database
summary
OligoArrayDb
Pangenomic sets of microarray probes for organisms with fully sequenced genomes
database
summary
OMA
Altenhoff, Adrian; Skunca, Nives; Glover, Natasha; Train, ClÃƒÂ©ment-Marie; Sueki, Anna; PiliÃ…Â¾ota, Ivana; Gori, Kevin; Tomiczek, Bartlomiej; MÃƒÂ¼ller, Steven; Redestig, Henning; Gonnet, Gaston; Dessimoz, Christophe
Orthology MAtrix
database
summary
OMA
Dessimoz, Christophe; Altenhoff, Adrian; Train, ClÃƒÂ©ment-Marie; Gilbert, Kimberly; Mediratta, Ishita; Mendes de Farias, Tarcisio; Moi, David; Nevers, Yannis; Radoykova, Hale-Seda; Rossier, Victor; Warwick Vesztrocy, Alex; Glover, Natasha
Orthologies across >2000 genomes
database
summary
OMA Orthology
Glover, Natasha; Altenhoff, Adrian; Warwick Vesztrocy, Alex; Train, Clement; Nicheperovich, Alina; Prieto BaÃ±os, Silvia; Julca, Irene; Moi, David; Nevers, Yannis; Majidian, Sina; Dessimoz, Christophe; Bernard, Charles
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem
database
summary
OMIA - Online Mendelian Inheritance in Animals
Nicholas F.W.
Catalog of animal genetic and genomic disorders
database
summary
OMPdb
Konstantinos D. Tsirigos
, Pantelis G. Bagos
and Stavros J. Hamodrakas
Beta-barrel outer membrane proteins from Gram-negative bacteria
database
summary
OncoDB
Wang, Xiaoyang; et al.
OncoDB v2.0: an expanded resource for exploring oncogenic mutations and clinical outcomes
database
summary
OncoDB
Minsu Cho , Gongyu Tang , Charles S Rogers , Makayla Dove , Xinyi Liu , Yuanxiang Li , Xiaowei Wang
OncoDB v2.0: an expanded resource for exploring oncogenic mutations and clinical outcomes
database
summary
OncoDB.HCC
Su WH, Chao CC, Yeh SH, Chen DS, Chen PJ, Jou YS
Oncogenomic database of hepatocellular carcinoma
database
summary
OncoMine
Cancer microarray data by gene or cancer type
database
summary
OncoSexome
Feng Zhu
Sex-based differences in cancer risk, biomarkers and reponses
database
summary
OncoSplicing
Xu, Hua; Zhang, Yangjun; Yao, Xiangyang; Zhou, Hui'.; Wu, Xiaoliang; Tian, Jianbo; Zeng, Jin; Yan, Libin; Duan, Chen; Liu, Haoran,; Li, Heng '.; Chen, Ke; Hu, Zhiquan; Ye, Zhangqun
Alternative splicing and cancer
database
summary
OncoVar
Mao, Fengbiao,; Wang, Tao21; Zhao, Xiaolu; Zhong, Jianing; Shi, Xiaohui; Teng, Huajing.; Ruan, Shasha; You, Mingcong; Sun, Zhongsheng
Driver mutations, genes and pathways in cancer
database
summary
ONQUADRO
Szachniuk, Marta; Zok, Tomasz; Kraszewska, Natalia; Miskiewicz, Joanna; Pielacinska, Paulina; Zurkowski, Michal
DNA and RNA quadruplexes
database
summary
OnTheFly
Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S.; Honig, Barry
DNA-binding specificities of transcription factors in Drosophila
database
summary
Ontobee
Edison Ong
, Zuoshuang Xiang
, Bin Zhao
, Yue Liu
, Yu Lin
, Jie Zheng
, Chris Mungall
, MÃƒÂ©lanie Courtot
, Alan Ruttenberg
, Yongqun He
Ontology database server of OBO Foundry
database
summary
ooTFD
Ghosh D.
Transcription factors and gene expression
database
summary
Open Genes
Rafikova, Ekaterina; Nemirovich-Danchenko, Nikolay; Ogmen, Anna; Parfenenkova, Anna; Velikanova, Anastasiia; Tikhonov, Stanislav; Peshkin, Leonid; Rafikov, Konstantin; Spiridonova, Olga; Belova, Yulia; Glinin, Timofey; Egorova, Anastasia; Batin, Mikhail
Open Genes â€” A New Comprehensive Database of Human Genes Associated With Aging and Longevity
database
summary
Open Proteomics Database
Mass-spectrometry-based proteomics data for human, yeast,
E.coli
and
Mycobacterium
database
summary
Open Targets
David Ochoa
1,2
, Andrew Hercules
1,2
, Miguel Carmona
1,2
, Daniel Suveges
1,2
Asier Gonzalez-Uriarte
1,2
, Cinzia Malangone
1,2
, Alfredo Miranda
1,2
, Luca Fumis
1,2
Denise Carvalho-Silva
1,2
, Michaela Spitzer
1,2
, Jarrod Baker
1,2
, Javier Ferrer
1,2
Arwa Raies
1,2
, Olesya Razuvayevskaya
1,2
, Adam Faulconbridge
1,2
, Eirini Petsalaki
1,2
Prudence Mutowo
2,3
, Sandra Machlitt-Northen
2,3
, Gareth Peat
1,2
, Elaine McAuley
1,2
Chuang Kee Ong
1,2
, Edward Mountjoy
2,4
, Maya Ghoussaini
2,4
, Andrea Pierleoni
1,2
Eliseo Papa
2,5
, Miguel Pignatelli
1,2
, Gautier Koscielny
2,3
, Mohd Karim
2,4
Jeremy Schwartzentruber
2,4
, David G. Hulcoop
2,3
, Ian Dunham
1,2,4
and Ellen M. McDonagh
1,2
Target Validation platform: links between potential drug targets and diseases
database
summary
Open Targets
Ochoa, David; Hercules, Andrew; Carmona, Miguel; Suveges, Daniel; Baker, Jarrod; Malangone, Cinzia; Lopez, Irene; Miranda, Alfredo; Cruz-Castillo, Carlos; Fumis, Luca; Bernal-Llinares, Manuel; Tsukanov, Kirill; Cornu, Helena; Tsirigos, Konstantinos; Razuv
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
database
summary
Open Targets
Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; Theo Platt; Francis Rowland; Priyanka Wankar; A. Patricia Bento; Tony Burdett; Antonio Fabregat; Simon Forbes; Anna Gaulton; Cristina Yenyxe Gonzalez; Henning Hermjakob; Anne Hersey; Steven Jupe; Senay Kafkas; Maria Keays; Catherine Leroy; Francisco-Javier Lopez; Maria Paula Magarinos; James Malone; Johanna McEntyre; Alfonso Munoz-Pomer Fuentes; Claire O'Donovan; Irene Papatheodorou; Helen Parkinson; Barbara Palka; Justin Paschall; Robert Petryszak; Naruemon Pratanwanich; Sirarat Sarntivijal; Gary Saunders; Konstantinos Sidiropoulos; Thomas Smith; Zbyslaw Sondka; Oliver Stegle; Y. Amy Tang; Edward Turner; Brendan Vaughan; Olga Vrousgou; Xavier Watkins; Maria-Jesus Martin; Philippe Sanseau; Jessica Vamathevan; Ewan Birney; Jeffrey Barrett; Ian Dunham
Open Targets has designed and developed a data integration and visualizatio
database
summary
Open Targets Genetics
Dunham, Ian; Ghoussaini, Maya; Mountjoy, Edward; Carmona, Miguel; Peat, Gareth; Schmidt, Ellen; Hercules, Andrew; Fumis, Luca; Miranda, Alfredo; Carvalho-Silva, Denise; Buniello, Annalisa; Burdett, Tony; Hayhurst, James D; Baker, Jarrod; Ferrer, Javier; G
Drug targets prioritised from genetic data
database
summary
Open TG-GATEs
Yamada, Hiroshi; Igarashi, Yoshinobu; Nakatsu, Noriyuki; Yamashita, Tomoya; Ono, Atsushi; Ohno, Yasuo; Urushidani, Tetsuro
Gene expression and toxicology data for rat liver and human and rat hepatocytes
database
summary
OpenProt
Roucou, Xavier; Leblanc, SÃ©bastien; Yala, Feriel; Lucier, Jean-FranÃ§ois; Levesque, Maxime; Provencher, Nicolas; Lapointe, Xavier; Jacques, Jean-FranÃ§ois; Fournier, Isabelle; Salzet, Michel; Ouangraoua, Aida; Scott, Michelle; Boisvert, Francois-Michel; Brunet, Marie
OpenProt 2.0 builds a path to the functional characterization of alternative proteins
database
summary
OpenTein
Nakai, Kenta; Park, Sung-Joon; Komiyama, Yusuke; Suemori, Hirofumi; Umezawa, Akihiro
Open Teratoma Investigation: images of teratomas derived from stem cells
database
summary
OPIA
Song, Shuhui; Cao, Yongrong; Tian, Dongmei; Tang, Zhixin; Liu, Xiaonan; Hu, Weijuan; Zhang, Zhang
OPIA: an open archive of plant images and related phenotypic traits
database
summary
OPM
Andrei L. Lomize
Orientations of Proteins in Membranes database
database
summary
OPTIC
Orthologous and Paralogous Transcripts in Clades
database
summary
ORegAnno
Open REGulatory ANNOtation database
database
summary
ORENZA
Lespinet O. and Labedan B.
Web resource for studying ORphan ENZyme Activities
database
summary
ORFDB
Collection of ORFs that are sold by Invitrogen
database
summary
Organ System Heterogeneity DB
Campillos, Monica; Mannil, Deepthi; Vogt, Ingo; Prinz, Jeanette
Phenotypic effects of diseases and drugs on different organs
database
summary
Organelle DB
Wiwatwattana N., Landau C., Cope G.J., Harp G., and Kumar A.
Organelle proteins and subcellular structures
database
summary
Organelle genomes
Organelle genome resource at NCBI
database
summary
OrganoidDB
Pan, Jianbo; Ma, Qinfeng; Tao, Haodong; Li, Qiang; Zhai, Zhaoyu; Zhang, Xuelu; Lin, Zhewei; Kuang, Ni
Organoid transcriptomics
database
summary
OrgXenomics
Feng Zhu
Proteomics of organoids and xenografts
database
summary
OriDB - The DNA Replication Origin Database
Nieduszynski, Conrad; Siow, Cheuk; Nieduszynska, Sian; MÃƒÆ’Ã‚Â¼ller, Carolin
Confirmed and predicted DNA replication origin sites
database
summary
oriTDB
Hong-Yu Ou
Origin-of-transfer regions of bacterial mobile genetic elements
database
summary
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species
BenoitÃ‚Â Bouvrette, Louis Philip;Bovaird, Samantha;Blanchette, Mathieu;LÃƒÂ©cuyer, Eric
No description supplied
database
summary
OrthoDB
Kuznetsov, Dmitry; Tegenfeld, Fredrik; Manni, Mose; Seppey, Mathieu; Berkeley, Matthew; Kriventseva, Evgenia; Zdobnov, Evgeny
OrthoDB v11: annotation of orthologs in the widest sampling of organismal d
database
summary
OrthoDB
Kriventseva, Evgenia; Zdobnov, Evgeny; Kuznetsov, Dmitry; Tegenfeld, Fredrik; Manni, Mose; Berkeley, Matthew
A hierarchical catalogue of orthologous proteins in fungal, plant, archaeal, bacterial and viral species
database
summary
OrtholugeDB
Whiteside, M.D., Winsor, G.L., Laird, M.R., Brinkman, F.S.L.
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
database
summary
OrthoMAM
Scornavacca, Celine; Allio, RÃ©mi; Delsuc, FrÃ©dÃ©ric; Belkhir, Khalid; Douzery, Emmanuel; Ranwez, Vincent
OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics
database
summary
OryGenesDB
Rice genes, T-DNA and Ds flanking sequence tags
database
summary
OverGeneDB
Makalowska, Izabela; Rosikiewicz, Wojciech; Suzuki, Yutaka,
No description supplied
database
summary
P-MITE
Chen, Jiongjiong; Hu, Qun; Zhang, Yu; Lu, Chen; Kuang, Hanhui
Plant miniature inverted-repeat transposable elements (MITEs)
database
summary
P10K
Miao, Wei; Gao, Xinxin; Chen, Kai; Xiong, Jie,'; Zou, Dong; Yang, Fangdian; Ma, Yingke; Jiang, Chuanqi; Gao, Xiaoxuan; Wang, Guangying; Gu, Siyu; Zhang, Peng; Luo, Shuai; Huang, Kaiyao; Bao, Yi-Ming; Zhang, Zhang; Ma, Lina
The P10K Database: A Data Portal for the Protist 10,000 Genomes Project
database
summary
P2CS
Barakat, Mohamed; Ortet, Philippe; Whitworth, David E.; Santaella, Catherine; Achouak, Wafa
Prokaryotic 2-Component Systems database
database
summary
P3DB
Xu, Dong; Yao, Qiuming; Ge, Huangyi; Wu, Shangquan; Zhang, Ning;; Chen, Wei; Xu,
Plant protein phosphorylation database
database
summary
PA-GOSUB
Protein sequences from model organisms, GO assignment and subcellular localization
database
summary
PAGER 2.0
Chen, Jake; Yue, Zongliang; Zheng, Qi; Neylon, Michael; Yoo, Minjae; Shin, Jimin; Zhao, Zhiying; Tan, Aik-Choon
No description supplied
database
summary
PAGER-COV
Chen, Jake Yue; Yue, Zongliang; Zhang, Eric; Xu, Clark; Khurana, Sunny; Batra, Nishant; Dang, Son; James, Cimino
Pathways and gene lists related to COVID-19
database
summary
PAIDB - Pathogenicity Island Database
Yoon, Sung Ho; Park, Young-Kyu; Kim, Jihyun F.
Pathogenicity islands in bacterial genomes
database
summary
PAIR
Mingzhi Lin
, Xueling Shen
and Xin Chen
1,2
Predicted Arabidopsis Interactome Resource
database
summary
Pairpot
Jian Liu
Paired spatial and single-cell transcriptomics
database
summary
PALI
Rakesh R., Bhaskara R. M., and Srinivasan N.
A Database of pairwise and multiple structural alignments of memnbers of protein domain families of known 3-D structured and structure based phylogenies. Alignments involving members of domain families with not necessarily known 3-D structure are also available in the database.
database
summary
PAMDB
Wilks, Angela; Huang, Weiliang; Brewer, Luke; Jones, Jace; Nguyen, Angela; Marcu, Ana; Wishart, David; Oglesby-Sherrouse, Amanda; Kane, Maureen
A comprehensive Pseudomonas aeruginosa metabolome database
database
summary
PancanQTL
Han, Leng; Gong, Jing'; Mei, Shufang; Liu, Chun-Jie; Xiang, Yu; Ye, Youqiong; Zhang, Zhao; Feng, Jing; Liu, Renyan; Diao, Lixia; Guo, Anyuan; Miao, Xiaoping
No description supplied
database
summary
PancanQTL
Han, Leng; Chen, Chengxuan; Liu, Yuan; Luo, Mei; Yang, Jingwen; Chen, Yamei; Wang, Runhao; Zhou, Joseph; Zang, Yong; Diao, Lixia
PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers
database
summary
Pancreas Expression
Chelala, Claude; Dayem Ullah, Abu; Cutts, Rosalind; Ghetia, Millika; Gadaleta, Emanuela; Hahn, Stephan; Crnogorac-Jurcevic, Tatjana; Lemoine, Nicholas
Pancreatic Expression database
database
summary
Pancreas Genome Pheome Atlas
Chelala, Claude; Marzec, Jacek; Dayem Ullah, Abu; PirrÃƒÂ², Stefano; Gadaleta, Emanuela; Lemoine, nicholas; Kocher, Hemant
The Pancreatic Expression Database
database
summary
PANDIT
Protein and associated nucleotide domains with inferred trees
database
summary
PanKB
Patrick Pahneuf
Microbial pangenomes
database
summary
PANTHER
Thomas, Paul; Mi, Huaiyu'; Ebert, Dustin; Muruganujan, Anushya; Mills, Caitlin; Albou, Laurent-Philippe; Mushayahama, Tremayne
Protein sequence evolution mapped to functions and pathways
database
summary
PANZEA
Zhao W.
, Canaran P.
, Jurkuta R.
, Fulton T.
, Glaubitz J.
, Buckler E.
3,4
, Doebley J.
, Gaut B.
, Goodman M.
, Holland J.
6,7
, Kresovich S.
, McMullen M.
8,9
, Stein L.
and Ware D.
1,4
Maize genome project data
database
summary
Papillomavirus Episteme
Alison McBride
A database of Papillomaviridae family of viruses
database
summary
ParameciumDB
Arnaiz 0. and Sperling L.
Paramecium
genome sequencing project
database
summary
PartiGeneDB
Assembled partial genomes for ~250 eukaryotic organisms
database
summary
PASS2
Sowdhamini, Ramanathan; Gandhimathi, Arumugam; Nair, Anu
Structural motifs of protein superfamilies
database
summary
PAT
Zhang, Zheng; Liu, Ya; Liu, Sheng; Pan, Zhuo; Ren, Yu; Jiang, Yiru; Wang, Feng; Li, Dan-dan; Li, Yue-zhong
Prokaryotic Antimicrobial Toxin database
database
summary
PathBank
Wishart, David S.; Li, Carin; Marcu, Ana; Hasan, Badran; Pon, Allison; Budinski, Zachary; Patron, Jonas; Lipton, Debra; Cao, Xuan; Oler, Eponine; Li, Krissa; Paccoud, MaÃƒÂ¯lys; Hong, Chelsea; Guo, An Chi; Chan, Christopher; Wei, William; Ramirez-Gaona, Miguel
PathBank is a new, comprehensive, visually rich pathway database containing
database
summary
PathBank
Wishart, David ; Kruger, Ray; Sivakumaran, Aadhavya; Harford, Karxena; Sanford, Selena; Doshi, Rahil; Khetarpal, Nitya; Fatokun, Omolola; Doucet, DaphnÃ©e; Zubkowski, Ashley; Jackson, Hayley; Sykes, Gina; Ramirez, Miguel; Marcu, Anna; Liang, Carin; Yee, Kristen; Garros, Christiana; Yahya Rayat, Dorsa; Coleongco, Jeanne; Nandyala, Tharuni; Gautam, Vasuk; Oler, Eponine
PathBank 2.0 â€“ The Pathway Database for Model Organism Metabolomics
database
summary
PathBase
European mutant mice pathology database: histopathology photomicrographs and macroscopic images
database
summary
pathDIP
Rahmati, Sara; Abovsky, Mark; Pastrello, Chiara; Jurisica, Igor
Pathway data integration and analysis portal
database
summary
PathDIP
Jurisica, Igor; Pastrello, Chiara; Kotlyar, Max; Abovsky, Mark; Lu, Richard
PathDIP 5: Improving coverage and making enrichment analysis more biologically meaningful.
database
summary
Pathguide
Bader G.D., Cary M.P. and Sander C.
A listing of pathway, signal transduction and protein-protein interaction databases
database
summary
PathoPlantÃ‚Â®
BÃƒÂ¼low L.
, Schindler M.
and Hehl R.
Signal transduction related to plant-pathogen interactions
database
summary
PathoYeastract
Teixeira, Miguel Monteiro, Pedro Tiago; Pais, Pedro; Costa, Catarina; Manna, Sauvagya; SÃƒÂ¡-Correia, Isabel
Transcription regulation in pathogenic yeasts
database
summary
Pathway Commons
Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor Rodchenkov, ÃƒÆ’Ã¢â‚¬â€œzgÃƒÆ’Ã‚Â¼n Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, and Chris Sander
Metabolic and signaling pathways from multiple organisms
database
summary
PATRIC, the bacterial bioinformatics database and analysis resource
Alice R. Wattam
, David Abraham
, Oral Dalay
, Terry L. Disz
2, 3
, Timothy Driscoll
, Joseph L. Gabbard
1, 4
, Roger Gough
, Deborah Hix
, Ronald Kenyon
, Dustin Machi
, Chunhong Mao
, Eric K. Nordberg
, Robert Olson
2, 3
, Ross Overbeek
3, 5
, Gordon D. Pusch
, Maulik Shukla
, Julie Schulman
, Rick L. Stevens
2, 6
, Daniel E. Sullivan
, Veronika Vonstein
, Andrew Warren
, Rebecca Will
, Meredith J.C. Wilson
, Hyun Seung Yoo
, Chengdong Zhang
, Yan Zhang
1, Bruno W. Sobral
1, 7
PathoSystems Resource Integration Center
database
summary
Patrocles
Samuel Hiard, Carole Charlier, Wouter Coppieters, Michel Georges, and Denis Baurain
Polymorphic miRNA-mediated gene regulation in vertebrates
database
summary
PAZAR
Transcription factors and regulatory sequence annotations
database
summary
PBMCpedia
Frederike Grandke; et al.
PBMCpedia: A harmonized PBMC scRNA-seq database with Unified Mapped Cells Labels
database
summary
PBmice
piggyBac transposon insertions in the mouse genome.
database
summary
PCAT
Zheng, Siyuan; Yang, Juechen; Li, Qilin; Noureen, Nighat; Fang, Yanbing; Kurmasheva, Raushan; Houghton, Peter; Wang, Xiaojing1
Pediatric cancer transcriptome explorer
database
summary
PCDB
Ezequiel I. Juritz, Sebastian Fernandez Alberti, and Gustavo D. Parisi
Protein Conformational Diversity database
database
summary
PCDDB
Lee Whitmore, Benjamin Woollett, Andrew John Miles, D.P. Klose, Robert W. Janes, and B. A. Wallace
Protein Circular Dichroism Database
database
summary
PceRBase
Chen, Ming; Yuan, Chunhui ,; Meng, XianWen; Li, Xue; Illing, Nicola; Ingle, Robert; Wang, Jingjing
Competing endogenous RNAs in plants
database
summary
PCOSKB
Idicula-Thomas, Susan; JOSEPH, SHAINI; BARAI, RAM SHANKAR; Bhujbalrao, Rasika
Genes, diseases, and pathways associated with PolyCystic Ovary Syndrome
database
summary
PCRPi-DB
Joan Segura and Narcis Fernandez-Fuentes
Presaging Critical Residues in Protein interface DataBase
database
summary
PCSD
Su, Zhen; Liu, Yue'; Tian, Tian'; Zhang, Kang.,; You, Qi; Yan, Hengyu; Zhao, Nannan; Yi, Xin; Xu, Wenying
No description supplied
database
summary
pcsRNADB
ZHOU, J; et al.
pcsRNADB: a comprehensive database for prokaryotic small RNA-target interactions
database
summary
PDB facilities
Touw, Wouter; Baakman, Coos; Black, Jon; te Beek, Tim; Krieger, Elmar; Joosten, Robbie; Vriend, Gert
Database of secondary structures of proteins
database
summary
PDB-Ligand
Jae-Min Shin and Doo-Ho Cho
3D structures of small molecules bound to proteins and nucleic acids
database
summary
PDB-REPRDB
Noguchi, T., Akiyama, Y.
Representative protein chains, based on PDB entries
database
summary
PDB_TM
GÁbor E. TusnÁdy, Zsuzsanna DosztÁnyi and IstvÁn Simon
Transmembrane proteins with known 3D structure
database
summary
PDBe
Armstrong, David R;Berrisford, John M;Conroy, Matthew J;Gutmanas, Aleksandras;Anyango, Stephen;Choudhary, Preeti;Clark, Alice R;Dana, Jose M;Deshpande, Mandar;Dunlop, Roisin;Gane, Paul;GÃƒÂ¡borovÃƒÂ¡, Romana;Gupta, Deepti;Haslam, Pauline;KoÃ„\x8Da, Jaroslav;Mak, Lora;Mir, Saqib;Mukhopadhyay, Abhik;Nadzirin, Nurul;Nair, Sreenath;Paysan-Lafosse, Typhaine;Pravda, Lukas;Sehnal, David;Salih, Osman;Smart, Oliver;Tolchard, James;Varadi, Mihaly;Svobodova-VaÃ…â„¢ekovÃƒÂ¡, Radka;Zaki, Hossam;Kleywegt, Gerard J;Velankar, Sameer
Protein Data Bank in Europe
database
summary
PDBe
Armstrong, David R;Berrisford, John M;Conroy, Matthew J;Gutmanas, Aleksandras;Anyango, Stephen;Choudhary, Preeti;Clark, Alice R;Dana, Jose M;Deshpande, Mandar;Dunlop, Roisin;Gane, Paul;GÃƒÂ¡borovÃƒÂ¡, Romana;Gupta, Deepti;Haslam, Pauline;KoÃ„\x8Da, Jaroslav;Mak, Lora;Mir, Saqib;Mukhopadhyay, Abhik;Nadzirin, Nurul;Nair, Sreenath;Paysan-Lafosse, Typhaine;Pravda, Lukas;Sehnal, David;Salih, Osman;Smart, Oliver;Tolchard, James;Varadi, Mihaly;Svobodova-VaÃ…â„¢ekovÃƒÂ¡, Radka;Zaki, Hossam;Kleywegt, Gerard J;Velankar, Sameer
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the
database
summary
PDBe-KB
Varadi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, Mandar; Nadzirin, Nurul; Nair, Sreenath; Pravda, LukÃ¡Å¡; Tanweer, Ahsan; Al-Lazikani, Bissan; Andreini, Claudia; Barton, Geoffrey; Bednar, David; Berka, Kar
PDBe-KB: Collaboratively defining the biological context of structural data
database
summary
PDBflex
Godzik, Adam; Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya A; Rotkiewicz, Piotr; Jaroszewski, Lukasz
Flexibility in protein structures
database
summary
PDBj
Haruki Nakamura
Protein Data Bank Japan
database
summary
PDBselect
Heinz-Uwe Hobohm
Representative protein structures with low sequence identity
database
summary
PDBSite
3D structure of protein functional sites
database
summary
PDBsum
Laskowski, R.A.
Summaries and analyses of PDB structures
database
summary
PDCdb
Leo Han
Peptide-drug conjugates
database
summary
PDCM Finder
Perova, Zinaida; Martinez, Mauricio; Lopez Gomez, Federico; Halmagyi, Csaba; Follette, Alex; Mason, Jeremy; Mandloi, Tushar; Neuhauser, Steven; Krupke, Debra; Begley, Dale; Bult, Carol; Parkinson, Helen; Groza, Tudor
Patient-Derived Cancer Models
database
summary
PDZBase
Protein-protein interactions involving PDZ domains
database
summary
pE-DB
Tompa, Peter; Lazar, Tamas; MartÃƒÂnez-PÃƒÂ©rez, Elizabeth; Quaglia, Federica; Hatos, Andras; Chemes, Lucia; Bernado, Pau; Blackledge, Martin; Cordeiro, Tiago; Fagerberg, Eric; Forman-Kay, Julie; Silvina, Marina; Garrone, Nicolas; Gibson, Toby; Gomes, Gregory;
Protein Ensemble Database: ensembles of intrinsically disordered and of unfolded proteins
database
summary
PEC - Profiling of
E. coli
Chromosome
Comprehensive database on
E. coli
genome
database
summary
PED
Hamidreza Ghafouri , Tamas Lazar , Alessio Del Conte , Luiggi G Tenorio Ku , PED Consortium , Peter Tompa , Silvio C E Tosatto , Alexander Miguel Monzon
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins
database
summary
PedAM
Ni, Xin; Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Guo, Dongming; Liang, Yunxiang; Tai, Jun; Chen, Geng'; Jin, Yaqiong; Liu, Zhimei; Shi, Tieliu
No description supplied
database
summary
PEDANT
Frishman, D.
, Mokrejs, M.
, Kosykh, D.
, KastenmÃƒÆ’Ã†â€™Ãƒâ€šÃ‚Â¼ller, G.
, Kolesov, G.
, Zubrzycki, I.
, Gruber, C.
, Geier, B.
, Kaps, A.
, Albermann, K.
, Volz, A.
, Wagner, C.
, Fellenberg, M.
, Heumann, K.
, Mewes, H.-W.
Automated analysis of genomic sequences
database
summary
PEDE - Pig Expression Data Explorer
Uenishi H.
1,3
, Eguchi-Ogawa T.
1,3
, Shinkai H.
2,3
, Okumura N.
2,3
, Suzuki K.
2,3
, Toki D.
2,3
, Hamasima N.
1,3
, Awata T.
1,3
Full-length pig cDNA libraries and ESTs
database
summary
PepCyber:P~Pep
Human protein interactions mediated by phosphoprotein-binding domains
database
summary
PepSeeker
Peptide identification and ion information from proteome experiments
database
summary
Peptaibol
Whitmore, L., Wallace, B.A.
Peptaibol (antibiotic peptide) sequences
database
summary
PeptideAtlas
Desiere F., Deutsch E.W., King N.L., Nesvizhskii A.I, Mallick P., Eng J., Chen S., Eddes J., Loevenich S.N., and Aebersold R.
Peptides identified in LC-MS/MS proteomics experiments
database
summary
PepX
Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, and Frederic Rousseau
A non-redundant database of protein-peptide complexes
database
summary
PeroxiBase
Peroxidases from plants, bacteria and fungi
database
summary
PeroxisomeDB
SchlÜter A.
, Fourcade S.
, DomÈnech-EstÉvez E.
, GabaldÓn T.
, Huerta-Cepas J.
, Berthommier G.
, Ripp R.
, Wanders R.J.A.
, Poch O.
and Pujol A.
1,5
Peroxisomal proteins, metabolic routes and diagnostic tools
database
summary
PerSADE
Han, Lianyi; et al.
PerSADE: personalized adverse drug event and its underlying molecular mechanisms
database
summary
PertOrg
Pan, Jianbo; Zhai, Zhaoyu; Zhang, Xuelu; Zhou, Lu; Lin, Zhewei; Kuang, Ni; Li, Qiang; Ma, Qinfeng; Tao, Haodong; Gao, Jieya; Ma, Shiyong
Changes induced in model organisms by in vivo genetic perturbation
database
summary
PerturBase
Qi Liu
Single-cell perturbation data
database
summary
PerturbAtlas
Ran Zhou
Bulk genetic perturbation data
database
summary
PerturbDB
Dong Yin
Perturb-seq data for gene function and drig target identification
database
summary
Peryton
Hatzigeorgiou, Artemis; Skoufos, Giorgos; Kardaras, Filippos; Alexiou, Athanasios; Kavakiotis, Ioannis; Lambropoulou, Anastasia; Kotsira, Vasiliki; Tastsoglou, Spyros
Microbe-disease associations
database
summary
Pfam
Mistry, Jaina; Chuguransky, Sara; Williams, Lowri; Qureshi, Matloob; Salazar, Gustavo; Sonnhammer, Erik; Tosatto, Silvio; Paladin, Lisanna; Raj, Shriya; Richardson, Lorna; Finn, Robert; Bateman, Alex
Now available thourgh InterPro
database
summary
PFCSDB
K.S.Egorova, P.V.Toukach
P{lant and Fungal Carbohydrate Structure Database
database
summary
PFD - Protein Folding Database
Buckle A.M.
Experimental data on protein folding
database
summary
PGDB
Prostate and prostatic diseases gene database
database
summary
PGDD
Chet, Peng; Wang, Xiaoxiao; et al.
Plant Genome Duplication Database,
database
summary
PGG.MHC
Xu, Shuhua; Zhao, Xiaohan; Ma, Sen; Jiang, Xuetong; Wang, Baonan
Population genetics of HLA genes
database
summary
PGG.Population
Xu, Shuhua; Zhang, Chao'; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan'; Deng, Lian; Tian, Lei; Feng, Qidi
No description supplied
database
summary
PGG.SV
Xu, Shuhua; Wang, Yimin; Ling, Yunchao; Gong, Jiao; Zhao, Xiaohan; Zhou, Hanwen; Xie, Bo; Lou, Haiyi; Zhuang, Xinhao; Jin, Li `; Fan, Shaohua; Zhang, Guo-Qing
Human genome structural variants
database
summary
PGS-depot
Yang, Sheng; Cao, Chen; Zhang, Shuting; Wang, Jianhua; Tian, Min; Ji, Xiaolong; Huang, Dandan; Gu, Ning
PGS-Depot: a comprehensive resource for polygenic score constructed by summary statistics based methods
database
summary
PGxDB
Trinh Tun Duong
Pharmacogenomics
database
summary
PhageDive
Jorg Overmann
Bacteriophages and archaeal viruses
database
summary
PhageScope
LI, Shuaicheng; Wang, Ruohan; Yang, Shuo; Liu, Zhixuan; Zhang, Yuanzheng; WANG, XUEYING; Xu, Zixin; Wang, Jianping
PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations
database
summary
PharmacoDB
Haibe-Kains, Benjamin; Feizi, Nikta; Kadambat Nair, Sisira; Smirnov, Petr; Beri, Gangesh; Eeles, Christopher; Nasr Esfahani, Parinaz; Nakano, Minoru; Tkachuk, Denis; Mammoliti, Anthony; Gorobets, Evgeniya; Mer, Arvind Singh; Lin, Eva; Yu, Yihong; Martin,
PharmacoDB 2.0 : Improving scalability and transparency of in vitro pharmac
database
summary
PharmacoDB
Haibe-Kains, Benjamin; Smirnov, Petr; Kofia, Victor; Maru, Alexander; Freeman, Mark; Ho, Chantal; El-Hachem, Nehme; Adam, George-Alexandru; Ba-alawi, Wail; Safikhani, Zhaleh
Recent cancer pharmacogenomic studies profiled large panels of cell lines a
database
summary
PharmFreq
Roman Tremmel, Yitian Zhou, Mahamadou D Camara, Sofiene Laarif, Erik Eliasson, Volker M Lauschke
PharmFreq is a comprehensive resource designed to aggregate pharmacogenetic frequency data, focusing on genetic
polymorphisms in drug-metabolizing enzymes, drug transporters, and genes encoding the human major histocompatibility
complex (MHC). These genetic variants are critical contributors to inter-individual differences in drug efficacy and safety, which can
significantly vary across human populations. The database provides a global perspective on this pharmacogenetic diversity,
enabling researchers to explore patterns and assess the frequency of variations that influence drug responses across diverse
populations.
database
summary
PharmGKB
Altman R.B., Carrillo M.W., Gong M, Gor W., Hernandez-Boussard T., Holbert D., Kiuchi M., MacBride A., Murray T., Liu F., Thorn C.F., Woon M., Truong T., Zhou T. and Klein T.E.
Variation in drug response based on human variation
database
summary
PharmGWAS
Jia, Peilin; Hongen, Kang; Pan, Siyu; Lin, Shiqi; Yuan, Na
PharmGWAS: a GWAS-based knowledgebase for drug repurposing
database
summary
Pharos
Oprea, Tudor; Sheils, Timothy; Mathias, Stephen; Kelleher, Keith; Siramshetty, Vishal; Nguyen, Dac-Trung; Bologa, Cristian; Jensen, Lars,; Vidovic, Dusica; Koleti, Amar; Schurer, Stephan; Waller, Anna; Yang, Jeremy; Holmes, Jayme; Dharkar, Poorva; MathÃƒÂ©,
Heterogenous data on unstudied and understudied drug targets
database
summary
PhaSepDB
Li, Tingting; Hou, Chao; Wang, Xinxin; Xie, Haotai; Chen, Taoyu; Zhu, Peiyu; Xu, Xiaofeng1; You, Kaiqiang
PhaSepDB in 2022: annotating phase separation-related proteins with droplet
database
summary
PhaSePro
BÃƒÂ¡lint MÃƒÂ©szÃƒÂ¡ros, GÃƒÂ¡bor ErdÃ…â€˜s, BeÃƒÂ¡ta SzabÃƒÂ³, Ãƒâ€°va SchÃƒÂ¡d, Ãƒ\x81gnes Tantos, Rawan Abukhairan, TamÃƒÂ¡s HorvÃƒÂ¡th, Nikoletta Murvai, Orsolya P KovÃƒÂ¡cs, MÃƒÂ¡rton KovÃƒÂ¡cs, Silvio C E Tosatto, PÃƒÂ©ter Tompa, Zsuzsanna DosztÃƒÂ¡nyi, Rita Pancsa
Membraneless organelles (MOs) are dynamic liquid condensates that host a va
database
summary
PheLiGe
Aulchenko, Yurii; Shashkova, Tatiana; Pakhomov, Eugene; Gorev, Denis; Karssen, Lennart; Joshi, Peter
Genotype-phenotype associations
database
summary
PhenoM
Zhaolei Zhang
Morphological database of essential yeast genes
database
summary
PhenomicDB
Groth P.
, Pavlova N.
, Kalev I.
,Tonov S.
, Georgiev G.
, Pohlenz H.D.
andWeiss B.
A cross-species genotype/phenotype database
database
summary
PhenoModifier
Sun, Hong; Guo, Yangfan; Lan, Xiaoping; Jia, Jia; Cai, Xiaoshu; Zhang, Guoqing; Xie, Jingjing; Liang, Qian; Li, Yixue; Yu, Guangjun
PhenoModifier is a genetic modifier database for elucidating the genetic ba
database
summary
PhEVER
Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, and Christian Gautier
Phylogenetic Exploration of Viruses and their Evolutionary Relationships
database
summary
PHI-base
Urban, Martin
; Pant, Rashmi
; Raghunath, Arath
i; Irvine, Alistair
; Pedro, Helder
; Hammond-Kosack, Kim
Genes affecting pathogen-host interactions
database
summary
PHI-base
Urban, Martin; Cuzick, Alayne; Seager, James; Wood, Val; Rutherford, Kim; Yagwakote Venkatesh, Shilpa; Sahu, Jashobanta; Iyer, S.; Khamari, Lokanath; De Silva, Nishadi; Carbajo MartÃnez, Manuel; Pedro, Helder; Yates, Andrew; Hammond-Kosack, Kim
PHI-base in 2022: a multi-species phenotype database for Pathogenâ€“Host In
database
summary
phiSITE
Lubos Klucar, Matej Stano, and Matus Hajduk
Gene regulation in bacteriophages
database
summary
PHOSIDA
Florian Gnad, Jeremy Gunawardena, and Matthias Mann
Phosphorylation sites in various species identified by mass spectrometry
database
summary
PhosPhAt
Arabidopsis Protein Phosphorylation Site Database
database
summary
Phospho3D
Zanzoni A., Ausiello G., Via A., Gherardini P.F. and Helmer-Citterich M.
3D structures of protein phosphorylation sites
database
summary
PhosphoSItePlus
Sites of protein phosphorylation and other post-translational modifications
database
summary
PhycoCosm
Grigoriev, Igor; Hayes, Richard; Calhoun, Sara; Kamel, Bishoy; Wang, Alice; Ahrendt, Steven; Dusheyko, Serge; Nikitin, Roman; Mondo, Stephen; Salamov, Asaf; Shabalov, Igor; Kuo, Alan
Comparative genomics of algae
database
summary
PhyloFacts
Krishnamurthy N., Brown D., Kirshner D., Glanville J. and SjÃƒâ€“lander K.
Phylogenomic analysis of protein families
database
summary
PhylomeDB
Gabaldon, Toni; Fuentes, Diego; Molina, Manu; Chorostecki, Uciel; Capella-Gutierrez, Salvador; Marcet-Houben, Marina
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotat
database
summary
PhylomeDB
Gabaldon, Toni; Huerta-Cepas, Jaime; Capella-Gutierrez, Salvador; Pryszcz, Leszek; Marcet-Houben, Marina
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana
database
summary
PhyloPat
Phylogenetic patterns of genes from the Ensembl database
database
summary
PhytAMP
Data repository of plant natural antimicrobial peptides
database
summary
PhytoPath
Kersey, Paul (proxy) (contact); Pedro, Helder; Maheswari, Uma; McDowall, Mark; Urban, Martin; Hammond-Kosack, Kim; Staines, Daniel; Kulesha, Eugene; Cuzick, Alayne; Irvine, Alistair
Genomics of fungal, oomycete and bacterial phytopathogens
database
summary
PHYTOPROT
Clusters of predicted plant proteins
database
summary
Phytozome
David M Goodstein
JGI's platform for green plant genomics
database
summary
piCdb
Gebert, Daniel; Rosenkranz, David; Zischler, Hans
piRNA clusters
database
summary
PICKLES
Hart, Traver; Lenoir, Walter; Lim, Tassica
No description supplied
database
summary
PICKLES
Novak, Lance C; Chou, Juihsuan; Colic, Medina; Bristow, Christopher; Hart, Traver
PICKLES v3: the updated database of pooled in vitro CRISPR knockout library
database
summary
pico-PLAZA
Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, Van de Peer Y, Grimsley N, Piganeau G.
Genome database of microbial photosynthetic eukaryotes.
database
summary
PID
NCI-Nature Pathway Interaction Database
database
summary
PIDD
Wu D.
, Cui F.
, Jernigan R.
and Wu Z.
A database of protein inter-atomic distances
database
summary
PIECE
Yong Qiang Gu
Plant Intron Exon Comparison and Evolution
database
summary
PIG - Pathogen Interaction Gateway
Host-pathogen protein-protein interactions
database
summary
PigBioBank
Zhang, Zhe; Zeng, Haonan; Zhang, Wenjing; Lin, Qing; Gao, Yahui; Teng, Jinyan; Xu, Zhiting; Cai, Xiaotian; Zhong, Zhanming; Wu, Jun; Liu, Yuqiang; Diao, Shuqi; Wei, Chen; Gong, WenTao; Pan, Xiangchun; Li, Zedong; Huang, Xiaoyu; Chen, Xifan; Du, Jinshi; Zhao, Fuping; Zhao, Yunxiang; Ballester, Maria; Crespo-Piazuelo, Daniel; Amills, Marcel; Clop, Alex; Karlskov-Mortensen, Peter; Fredholm, Merete; Li, Pinghua; Huang, Ruihua; Tang, Guoqing; Li, Mingzhou; Liu, Xiaohong; Yaosheng, Chen; Zhang, Qin; Li, Jiaqi; Yuan, Xiaolong; Ding, Xiangdong; Fang, Lingzhao
PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs
database
summary
PigGIS
Ruan J.
1,2
, Guo Y.
1,2
, Li H.
, Hu Y.
, Song F.
, Huang X.
, Ma L.
1,2
, Kristiensen K.
, Bolund L.
1,4
and Wang J.
1,3,4
Pig genome mapping, genes and ESTs
database
summary
PINA
Jianmin Wu
Protein Interaction Network Analysis
database
summary
PINT
Shaji Kumar M.D.
and Gromiha M.M.
Protein-protein interactions thermodynamic database
database
summary
PIPdb
Wu Lin Huan
Plasmids in Pathogens Database
database
summary
PIPs
Predicted human protein-protein interactions
database
summary
PIR - Protein Information Resource
Wu C.H.
, Yeh L.S.
, Huang H.
and Barker W.C.
PIR protein sequence database, has been merged into UniProt Knowledgebase and UniParc
database
summary
piRBase
He, Shunmin; Wang, Jiajia"; Shi, YiRong; Zhou, Honghong; Zhang, Peng.'; Song, Tingrui; Ying, Zhiye; Yu, Haopeng; Li, Yanyan; Zhao, Yi; Zeng, Xiaoxi; Chen, Runsheng.
Database supporting piRNA functional study
database
summary
piRBase: a comprehensive database of piRNA sequences
Wang, Jiajia;Zhang, Peng;Lu, Yiping;Li, Yanyan;Zheng, Yu;Kan, Yunchao;Chen, Runsheng;He, Shunmin
No description supplied
database
summary
piRNABank
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat
database
summary
piRNAclusterDB
Rosenkranz, David
Clusters of piRNAs
database
summary
PIRSF
Natale, D.A.
, Arighi, C.
, Barker, W.C.
, Hu, Z. Z.
, Huang, H.
, Mazumder, R.
, Nikolskaya, A. N.
, Vasudevan. S.
, Vinayaka, C. R.
, Yeh, L.S.
, Wu, C. H.
PIR's family/superfamily classification of whole proteins
database
summary
piRTarBase: a database of piRNA targeting sites and their roles in gene regulation
Wu, Wei-Sheng;Brown, Jordan S;Chen, Tsung-Te;Chu, Yu-Han;Huang, Wei-Che;Tu, Shikui;Lee, Heng-Chi
No description supplied
database
summary
piSite
Database of Protein Interaction Sites using multiple binding states in PDB
database
summary
PIT-DB
Bessant, Conrad; Saha, Shyamasree; Chatzimichali, Eleni; Matthews, David
No description supplied
database
summary
PK-DB
KÃƒÂ¶nig, Matthias; Grzegorzewski, Jan; Brandhorst, Janosch; Green, Kathleen; Eleftheriadou, Dimitra; Duport, Yannick; Bartsch, Florian; KÃƒÂ¶ller, Adrian; Ke, Danny; De Angelis, Sara
Pharmacokinetics data from clinical trials and pre-clinical research
database
summary
PKDB - Pharmacokinetics Database
Jan Grzegorzewski, Janosch Brandhorst, Kathleen Green, Dimitra Eleftheriadou, Yannick Duport, Florian Barthorscht, Adrian KÃƒÂ¶ller, Danny (Yu Jia) Ke, Sara De Angelis and Matthias KÃƒÂ¶nig
Pharmacokinetics Database
database
summary
PLAbDab
Deane, Charlotte; Abanades, Brennan; Olsen, Tobias; Raybould, Matthew; Aguilar-Sanjuan, Broncio; Wong, Wing Ki; Georges, Guy; Bujotzek, Alexander
The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures
database
summary
PLAbDab-nano
Gemma Gordon
Nanobody sequences taken from patents and literature
database
summary
PLaMoM
Zhang, Shoudong; Guan, Daogang; Yan, Bin; Hua, Jingmin; Thieme, Christoph; Zhu, Hailong; Zhao, Zhongying,; Kragler, Friedrich; Xia, Yiji
Plant Mobile Macromolecules: Extracellular siRNAs, microRNAs, mRNAs and proteins in plants
database
summary
PLANdbAffy
Ramil N. Nurtdinov, Mikhail O. Vasiliev, Anna S. Ershova, Ilia S. Lossev, and Anna S. Karyagina
Probe-Level Annotation Database for Affymetrix microarrays
database
summary
Planet Microbe
Hurwitz, Bonnie; Ponsero, Alise; Bomhoff, Matthew; Blumberg, Kai; Youens-Clark, Ken; Herz, Nina; Wood-Charlson, Elisha; Delong, Ed
Oceanographic omics datasets linked to environmental metadata
database
summary
PlanMine
Rink, Jochen; Brandl, Holger; Moon, HongKee; Vila-FarrÃ¯Â¿Â½, Miquel; Liu, Shang-Yun; Henry, Ian
Platform for archiving and mining planarian biodiversity
database
summary
Plant DNA C-values database
Garcia, SÃƒÂ²nia; Leitch, Ilia; Anadon, Alba; Canela, Miguel; GÃƒÂ¡lvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Valles, Joan; Siljak-Yakovlev, Sonja; Vitales, Daniel; Bennett, Michael
Genome sizes of various plants and algae
database
summary
Plant editosome database: a curated database of RNA editosome in plants
Li, Man;Xia, Lin;Zhang, Yuansheng;Niu, Guangyi;Li, Mengwei;Wang, Pei;Zhang, Yang;Sang, Jian;Zou, Dong;Hu, Songnian;Hao, Lili;Zhang, Zhang
No description supplied
database
summary
Plant genome duplication database
Chet, Peng; Wang, Xiaoxiao; et al.
PGDD 2.0: Plant Genome Duplication Database with Updated Content and Tools
database
summary
Plant Metabolomics
Preeti Bais
Arabidopsis metabolomics database
database
summary
Plant MPSS
Nakano M.
, Nobuta K.
, Vemaraju K.
, Singh Tej S.
, Skogen J.W.
, and Meyers B.C.
1,2
Massively parallel signature sequencing of plant genes
database
summary
Plant Ontology database
Jaiswal P.
, Avraham S.
, Ilic K.
, Kellogg E.A.
, McCouch S.
, Pujar A.
, Reiser L.
, Rhee S.Y.
, Sachs M.M.
5,6
, Schaeffer M.
6,7
, Stein L.
, Stevens P.
4,8
, Vincent L.
, Ware D.
2,6
, Zapata F.
4,8
A controlled vocabulary of plant structures and growth stages
database
summary
Plant Organelles Database
Images of plant organelles and protocols for plant organelle research12
database
summary
Plant Reactome
Jaiswal, Pankaj; Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Wu, Guanming; Fabregat, Antonio; Elser, Justin; Weiser, Joel; Keays, Maria; MuÃƒÂ±oz-Pomer Fuentes, Alfonso; Petryszak, Robert; Stein, Lincoln; Ware, Doreen
Plant metabolic, regulatory and signaling pathways
database
summary
Plant Reactome
Naithani, Sushma; Gupta, Parul; Elser, Justin; Hooks, Elizabeth; D'Eustachio, Peter G; Jaiswal, Pankajunreliable
Plant Reactome Knowledgebase: Empowering plant pathway exploration and OMICS data analysis
database
summary
Plant repeat database
Repetitive sequences in plant genomes
database
summary
Plant snoRNA DB
snoRNA genes in plant species
database
summary
Plant Stress-Responsive Gene Catalog
Stress-responsive gene in various plant species
database
summary
Plant-ImputeDB
Gong, Jing; Gao, Yingjie; Yang, Wenqian; Yang, Zhiquan; Yang, Yanbo; Yang, Qing-Yong; Niu, Xiaohui
Reference panels and imputation methods for plant genomes
database
summary
PLANT-PIs
Consiglio A., Grillo G., Licciulli F., Ceci L.R., Liuni S., Losito N., Volpicella M., Gallerani R., and De Leo F.
Plant protease inhibitors
database
summary
PlantCellMarker
Cao, Peijian; jin, jingjing; Lu, Peng; Xu, Yalong; Tao, Jiemeng; Li, Zefeng; Wang, Shuaibin; Yu, Shizhou; Wang, Chen; Xie, Xiaodong; Gao, Junping; Chen, Qiansi; Wang, Lin; Pu, Wenxuan
Plant Cell Marker Database
database
summary
PlantCircRNA
Shutian He, Jianhao Bing, Yang Zhong, Xiaoyang Zheng, Ziyu Zhou, Yifei Wang, Jiming Hu and Xiaoyong Sun
Plant circular RNAs
database
summary
PlantDHS
Jiang, Jiming; Zhang, Tao; Marand, Alexandre
Plant DNase I hypersensitive Site Database
database
summary
Planteome
Jaiswal, Pankaj; Cooper, Laurel; Meier, Austin; Laporte, Marie; Mungall, Chris; Elser, Justin; Sinn, Brandon; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan; Qu, Botong; Smith, Barry; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John; Stevenson, Dennis; Arnaud, Elizabeth
Reference and species-specific ontologies for plants, with annotations to plant genomics,
phenomics and genetics data.
database
summary
Planteome
Jaiswal, Pankaj; Cooper, Laurel; Jaiswal, Pankajunreliable; Elser, Justin; Laporte, Marie; Arnaud, Elizabeth
Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology
database
summary
plantEXP
Dou, Daolong; liu, jinding; Zhang, Yaru; Zheng, Yiqing; Zhu, Yali; Guan, Zhuoran; Lang, Kun; Shen, Danyu; Huang, Wen
Plant gene (co-)expression and alternative splicing
database
summary
PlantGDB
Dong, Q.
, Schlueter, S.D.
, Brendel, V.
1,2
Actively-transcribed plant genomic sequences
database
summary
PlantGSAD
Su, Zhen; Ma, Xuelian; Yan, Hengyu; Yang, Jiaotong; Liu, Yue'; Li, Zhongqiu; Sheng, Menghao; Cao, Yaxin; Yu, Xinyue; Yi, Xin; Xu, Wenying
Plant gene set annotations
database
summary
PlantNATsDB
Ming Chen
Plant natural antisense transcripts
database
summary
PlantPAD
Hao, Ge-Fei; Dong, Xinyu; Zhao, Kejun; Wang, Qi; Wu, Xincaiinactive; Huang, Yuanqin; Wu, Xue; Dong, Yanwen; Zhang, Tianhan; Liu, Yingwei; Wang, Shuang; Yang, Xiaoyan; Chen, Dongyu; Gao, Yangyang; Yang, Jing; Chen, Panfen; Gao, Zhenran; Wu, Xian; Wang, Yong; Bai, Qinrong; Li, Shaobo
PlantPAD: a platform for large-scale image phenomics analysis of disease in plant science
database
summary
PlantPAN
Chang, Wen-Chi; Chow, Chi-Nga; Yang, Chien-Wen; Wu, Nai-Yun; Wang, Hung-Teng; Tseng, Kuan-Chieh; Chiu, Yu-hsuan; Lee, Tzong-Yi
PlantPAN 4.0: Updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters
database
summary
PlantPAN
Chang, Wen-Chi; Chow, Chi-Nga; Zheng, Han-Qin; Wu, Nai-Yun; Chien, Chia-Hung; Huang, Hsien-Da; Lee, Tzong-Yi; Chiang-Hsieh, Yi-Fan; Hou, Ping-Fu; Yang, Tien-Yi
Plant Promoter Analysis Navigator
database
summary
PlantProm
Plant promoter sequences
database
summary
PlantRNA
ValÃƒÆ’Ã‚Â©rie Cognat
, Gaël Pawlak
, Anne-Marie Duchêne, Magali Daujat, Anaïs Gigant, Thalia Salinas, Morgane Michaud, Bernard Gutmann, Philippe GiegÃƒÆ’Ã‚Â©, Anthony Gobert and Laurence MarÃƒÆ’Ã‚Â©chal-Drouard
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
database
summary
PlantsP/PlantsT
Tchieu, J.
, Fana, F.
, Fink, J.L.
, Harper, J.
, Nair, M.
, Niedner, R.H.
, Smith, D.W.
, Steube, K.
, Tam, T.
, Veretnik, S.
, Wang, D.
, Gribskov, M.
Functional genomics databases focusing on proteins involved in plant phosphorylation and membrane transport, respectively
database
summary
PlantTFDB
Jin, Jinpu; Tian, Feng; Yang, De-Chang; Meng, Yu-Qi; Kong, Lei; Luo, Jingchu; Gao, Ge
Plant Transcription Factor Database
database
summary
PlantTribes
Families of protein-coding genes from five sequenced plant species
database
summary
Plasma Proteome Database
Pandey, Akhilesh; Nanjappa, Vishalakshi; Thomas, Joji; Marimuthu, Arivusudar; Muthusamy, Babylakshmi; Radhakrishnan, Aneesha; Sharma, Rakesh; Khan, Aafaque; Balakrishnan, Lavanya; Sahasrabuddhe, Nandini; Kumar, Satwant; Jhaveri, Binit; Sheth, Kaushal; Khatana, Ramesh; Shaw, Patrick; Srikanth, Srinivas; Mathur, Premendu; Shankar, Subramanian; Nagaraja, Dindagur; Christopher, Rita; Mathivanan, Suresh; Raju, Rajesh; Sirdeshmukh, Ravi; Chatterjee, Aditi; Simpson, Richard; Harsha, H; T.S., Keshava Prasad
Qualitative and quantitative information on proteins in human plasma and serum
database
summary
PlasmID
A repository for collection and distribution of plasmid clones
database
summary
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data
Jesus, Tiago F;Ribeiro-GonÃƒÂ§alves, Bruno;Silva, Diogo N;Bortolaia, Valeria;Ramirez, MÃƒÂ¡rio;CarriÃƒÂ§o, JoÃƒÂ£o A
No description supplied
database
summary
PlasmidScope
Shuai Cheng Li
Plasmids with rich annotations
database
summary
PlasmoGEM
Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Bronner Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian; Billker, Oliver
DNA vectors and data for genetic manipulation of malaria parasites
database
summary
Plastid-LCGbase
Yu, Jun; Wang, Dapeng.
Plastid Lineage-based Conserved Gene-pair Database
database
summary
Platinum
Ascher, David; Pires, Douglas; Blundell, Tom
Experimentally measured effects of mutations on protein-ligand complexes
database
summary
PLAZA
Vandepoele, Klaas; Van Bel, Michiel; Diels, Tim; Vancaester, Emmelien; Kreft, Lukasz; Botzki, Alexander; Van de Peer, Yves; Coppens, Frederik
No description supplied
database
summary
PLAZA
Vandepoele, Klaas; Van Bel, Michiel; Silvestri, Francesca; Kreft, Lukasz; Botzki, Alexander; Weitz, Eric; Coppens, Frederik
PLAZA 5.0: extending the scope and power of comparative and functional geno
database
summary
PLAZA
Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; InzÃƒÂ©, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas
Comparative genomics of monocot and dicot plants
database
summary
PLEXdb
Julie Dickerson
Gene Expression Resources for Plants and Plant Pathogens
database
summary
PLPMDB
Pyridoxal-5'-phosphate dependent enzymes mutations
database
summary
PLprot
Arabidopsis thaliana
chloroplast protein database
database
summary
PLSDB
Keller, Andreas; Schmartz, Georges; Hartung, Anna; Hirsch, Pascal; Kern, Fabian; Fehlmann, Tobias; Mueller, Rolf
database of plasmids by NCBI
database
summary
PLSDB: a resource of complete bacterial plasmids
Galata, Valentina;Fehlmann, Tobias;Backes, Christina;Keller, Andreas
PLSDB: Advancing a
comprehensive database of bacterial plasmids"
database
summary
PMADS
Ying Zhou; et al.
PMADS: an integrated database of curated and proteomics-informed association for small molecule drugs
database
summary
PMAP
Proteolysis Map
database
summary
PMDB - Protein Model Database
Castrignano T.
, D'Onorio De Meo P.
, Cozzetto D.
, Talamo I. G.
and Tramontano, A.
2,3
3D protein models obtained from structure predictions
database
summary
PMDBase
Yu, Jingyin; Dossa, Komovi; Wang, Linhai; Zhang, Yanxin; Wei, Xin; Zhang, Xiurong
Plant microsatellites and marker development
database
summary
PMhub
Chen, Wei; Tian, Zhitao; Hu, Xin; Xu, Yingying; Liu, Mengmeng; Liu, Hongbo; Li, Dongqin; Hu, Lisong; Wei, Guo-Zh
PMhub 1.0: a comprehensive plant metabolome database
database
summary
PmiREN
Yang, Xiaozeng; Guo, Zhonglong; Kuang, Zheng; Zhao, Yongxin; Deng, Yang; He, Hao; Wan, Miaomiao; Tao, Yihan; Wang, Dong; Wei, Jianhua; Li, Lei
Plant miRNA encyclopedia
database
summary
PmiRKB
Yijun Meng
1,2,3
, Lingfeng Gou
, Dijun Chen
, Chuanzao Mao
, Yongfeng Jin
, Ping Wu
,and Ming Chen
1,2
Plant microRNA knowledge base
database
summary
PncsHub
Stubenrauch, Christopher; Dai, Wei2; Li, Jiahui; Li, Qi; Cai, Jiasheng; Su, Jianzhong; Wang, Jiawei
Non-classically secreted proteins in Gram-positive bacteria
database
summary
PNRD
Yi, Xin; Zhang, Zhenhai; Xu, Wenying; Su, Zhen
Plant Non-coding RNA Database
database
summary
Pocketome
Ruben Abagyan
Small-molecule and/or peptide binding pockets in the structural proteome
database
summary
POGO-DB
Rosen, Gail; Lan, Yemin; Morrison, Calvin; Hershberg, Ruth
Pairwise-comparisons Of Genomes and universal Orthologous genes
database
summary
POGs/PlantRBP
Walker N., Stiffler N., Barkan A.
Orthologous groups of RNA binding proteins in plants
database
summary
Pol3Base
Yang, Jian-Hua; Cai, Li; Xuan, Jiajia; Lin, Qiao; Wang, Junhao; Liu, Shu-Rong; Xie, Fangzhou; Zheng, Lingling; Li, Bin; Qu, Liang-Hu
PolIII-transcribed ncRNAs
database
summary
Polbase
Brad Langhorst
Biochemical, genetic, and structural information about DNA polymerases
database
summary
PolyA_DB
A database of mammalian mRNA polyadenylation
database
summary
PolyA_DB
Tian, Bin; Wang, Ruijia; Nambiar, Ram; Zheng, Dinghai
No description supplied
database
summary
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3Ã¢â‚¬Â² end sequencing
Herrmann, Christina J;Schmidt, Ralf;Kanitz, Alexander;Artimo, Panu;Gruber, Andreas J;Zavolan, Mihaela
Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isofor
database
summary
PolyDoms
Jegga A.G.
1,2
, Gowrisankar S.
1,3
, Chen J.
1,3
and Aronow B.J.
1,2,3
Human coding SNPs mapped onto protein domains
database
summary
PolymiRTS
Cui, Yan; Bhattacharya, Anindya; Ziebarth, Jesse
Polymorphism in microRNA Target Site
database
summary
PolyQ
Amy L. Robertson, Mark A. Bate, Steve G. Androulakis, Stephen P. Bottomley, and Ashley M. Buckle
Polyglutamine Repeats in Proteins
database
summary
PoMaMo - Potato Maps and More
Meyer S.
, Nagel A.
, Basekow, R.
, Gebhardt C.
A comprehensive database for potato genome data
database
summary
PomBase
McDowall, Mark; Harris, Midori; Lock, Antonia; Rutherford, Kim; Staines, Daniel; Bahler, Jurg; Kersey, Paul; Oliver, Stephen; Wood, Val
Genome database on S. pombe
database
summary
PopHuman
Casillas, SÃƒÂ²nia; Mulet, Roger; Villegas-MirÃƒÂ³n, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume; Laayouni, Hafid; Barbadilla, Antonio
The 1000 Genomes Project (1000GP) represents the most comprehensive world-w
database
summary
PopHumanVar
Casillas, SÃ²nia; Colomer-Vilaplana, Aina; Murga-Moreno, JesÃºs; Canalda-Baltrons, Aleix; Inserte, Clara; Soto, Daniel; Coronado-Zamora, Marta; Barbadilla, Antonio
Causal variants of selective sweeps
database
summary
PortEco
Hu, James C.; Sherlock, Gavin; Siegele, Deborah; Aleksander, Suzanne; Ball, Catherine; Demeter, Janos; Gouni, Sushanth; Liles, Nathan; McIntosh, Brenley; Mi, Huaiyu'; Muruganujan, Anushya; Wymore, Farrell; Thomas, Paul
Escherichia coli K-12 knowledgebase portal
database
summary
PoSSuM
Ito, Jun-ichi; Ikeda, Kazuyoshi; Yamada, Kazunori; Mizuguchi, Kenji; Tomii, Kentaro
Ligand-binding Pocket Similarity Search using Multiple-Sketches
database
summary
POSTAR
Lu, Zhi; Yang, Yu-Cheng; Hu, Boqin; Huang, Yiming; Zhu, Yumin
Post-transcriptional regulation by RNA-binding proteins
database
summary
POSTAR
Lu, Zhi; Zhao, Weihao; Zhang, Shang; Zhu, Yumin; Xi, Xiaochen; Bao, Pengfei; Ma, Ziyuan; Kapral, Thomas; Chen, Shuyuan; Zagrovic, Bojan; Yang, Yucheng
POSTAR3: an updated platform for exploring post-transcriptional regulation
database
summary
POSTAR2: deciphering the post-transcriptional regulatory logics
Zhu, Yumin;Xu, Gang;Yang, Yucheng T;Xu, Zhiyu;Chen, Xinduo;Shi, Binbin;Xie, Daoxin;Lu, Zhi John;Wang, Pengyuan
No description supplied
database
summary
Poxvirus.org
Poxvirus genomic sequences and gene annotation
database
summary
PPD
Toseland C.P., McSparron H., Doytchinova I.A., M.N.Davies, and Flower D.R.
Experimentally-determined protein pKa values
database
summary
ppdb
Yamamoto, Yoshiharu.; Hieno, Ayaka; Naznin, Hushna; Hyakumachi, Mitsuro; Sakurai, Tetsuya; Tokizawa, Mutsutomo; Koyama, Hiroyuki; Sato, Naoki; Nishiyama, Tomoaki; Hasebe, Mitsuyasu; Zimmer, Andreas; Lang, Daniel; Reski, Ralf; Rensing, Stefan; Obokata, Junichi
Plant promoter database
database
summary
PPDB: Plant Proteomics Database
Plant Proteomics Database
database
summary
PPGR
xie, Jianbo; Yang, Sen; Zong, Wenting; Shi, Lingling; Li, Ruisi; Ma, Zhenshu; Ma, Shubao; Si, Jingna; Wu, Zhijing; Zhai, Jinglan; Fan, Zhuojing; Chen, Sisi; Huang, Huahong; Zhang, Deqiang; Bao, Yi-Ming; Li, Rujiao
PPGR: a comprehensive perennial plant genomes and regulation database
database
summary
PPT-DB
Protein Property Prediction and Testing Database
database
summary
PR2
Richard Christen
Protist Ribosomal reference Database
database
summary
PRECOG and related resources
Andrew Gentles; et al.
PRECOG update: An augmented resource of clinical outcome associations for gene expression and mutations
database
summary
PRECOG and related resources
Gentles, Andrew; Benraad, Brooks A; Lalgudi, Chinmay; et al.
PRECOG update: An augmented resource of clinical outcome associations for gene expression and mutations
database
summary
Predictive Networks
John Quackenbush
Integration, navigation, visualization, and analysis of gene interaction networks
database
summary
PReMod
Predicted transcriptional regulatory modules in the human genome
database
summary
prePPI
Barry Honig
Predicted and experimentally determined protein-protein interactions for yeast and human
database
summary
PREX
Laura Soito, Chris Williamson, Stacy T. Knutson, Jacquelyn S. Fetrow, Leslie B. Poole, and Kimberly J. Nelson
PeroxiRedoxin classification indEX
database
summary
PRF
Protein research foundation database of peptides: sequences, literature and unnatural amino acids
database
summary
PRGdb
Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, and Maria Raffaella Ercolano
Plant disease resistance genes
database
summary
PRGdb
Ercolano, Maria; Osuna Cruz, Cristina; PaytuvÃƒÂ, Andreu; Di Donato, Antimo; Sundesha, Vicky; Andolfo, Giuseppe; Aiese Cigliano, Riccardo; Sanseverino, Walter
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been rede
database
summary
PRGdb
Ercolano, Maria; Calle GarcÃa, Joan; Guadagno, Anna; PaytuvÃ, Andreu; Saera-Vila, Alfonso; Amoroso, Ciro Giammaria; D'Esposito, Daniela; Andolfo, Giuseppe; Aiese Cigliano, Riccardo; Sanseverino, Walter
Plant Resistance Genes
database
summary
PRIDB
Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, and Drena Dobbs
Protein-RNA Interface Database
database
summary
PRIDE
Jones P.
, CÃƒÆ’Ã‚Â´tÃƒÆ’Ã‚Â© R.G.
, Martens L.
, Quinn A.F.
, Taylor C.F.
, Derache W.
, Hermjakob H.
and Apweiler R.
Proteomics peptide identification database
database
summary
PRIDE
Vizcaino, Juan Antonio; Perez-Riverol, Yasset; Bai, Jingwen; Bandla, Chakradhar; Garcia-Seisdedos, David; Hewapathirana, Suresh; Kamatchinathan, Selvakumar; Kundu, Deepti J.; Prakash, Ananth; Frericks-Zipper, Anika; Eisenacher, Martin; Walzer, Mathias; Wa
The PRIDE database resources in 2022: A Hub for mass spectrometry-based pro
database
summary
PRIME
Zhang, Zhizhuo; Zhao, Hongyu; Wang, Tao
Human-associated 16S rRNA microbiome amplicon sequencing data with harmonized phenotypic metadata and taxonomic abundance tables.
database
summary
PrimerBank
Athanasia Spandidos, Xiaowei Wang, Huajun Wang, and Brian Seed
PCR primers for human and mouse genes
database
summary
PRINTS
Attwood, T.K.
, Bradley, P.
1,2
, Gaulton, A.
, Maudling, N.
, Mitchell, A.
1,2
, Moulton, G.
Hierarchical gene family fingerprints
database
summary
Priority index
Fang, Hai; Knight, Julian
Drug targets for immune-mediated diseases
database
summary
Pristionchus.org
Dieterich C., Roeseler W., Sobetzko P. and Sommer R.J.
Genome data of the nematode
Pristionchus pacificus
database
summary
PRMD
Liu, Qi; Lang, Xiaoqiang; Yu, Chunyan; Mengyuan, Shen; Gu, Lei; Qian, Qian; Zhou, Degui; Tan, Jiantao; Li, Yiliang; Peng, Xin; Deng, Zhujun; Diao, Shu; Ruan, Zhaohui; Xu, Zhi; Xing, Junlian; Li, Chen; Ding, Changjun; Cao, Yi
PRMD: an integrated database for plant RNA modifications
database
summary
PRO
Natale, Darren; Arighi, Cecilia; Blake, Judith; Bult, Carol; Christie, Karen; Cowart, Julie; D'Eustachio, Peter; Diehl, Alexander; Drabkin, Harold; Helfer, Olivia; Huang, Hongzhan; Masci, AnnaMaria; Ren, Jia; Roberts, Natalia; Ross, Karen; Ruttenberg, Alan; Shamovsky, Veronica; Smith, Barry; Yerramalla, Meher; Zhang, Jian ,; AlJanahi, Aisha; Gan, Cynthia; ÃƒÆ’Ã¢â‚¬Â¡elen, Irem; Lv, Mengxi; Schuster-Lezell, Emily; Wu, Cathy H
Protein Ontology, encompasses a sub-ontology of proteins based on evolutionary relatedness (ProEvo) and a sub-ontology of the multiple protein forms produced from a given gene (ProForm)
database
summary
probeBase
Loy A., Maixner, F, Wagner M. and Horn M.
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information
database
summary
proCHiPdb
Palsson, Bernhard; Decker, Katherine; Gao, Ye; Rychel, Kevin; Al Bulushi, Tahani; Chauhan, Siddharth; Kim, Donghyuk,; Cho, Byung-Kwan
Chromatin immunoprecipitation database for prokaryotic organisms
database
summary
PROCOGNATE
Protein cognate ligands for the domains in enzyme structures
database
summary
ProDom
Courcelle E., Beausse Y., CarrÃƒÂ¨re, S., Bru C., Dalmar S., Kahn D.
Protein domain families
database
summary
PRODORIC
Dudek, Christian-Alexander; Jahn, Dieter
PRODORIC: state-of-the-art database of prokaryotic gene regulation
database
summary
PRODORIC
Prokaryotic database of gene regulation and regulatory networks
database
summary
PRODORIC2
Eckweiler, Denitsa; Dudek, Christian-Alexander; Hartlich, Juliane; Broetje, David; Jahn, Dieter
No description supplied
database
summary
Progenetix
Cai, Haoyang; Kumar, Nitin; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael Baudis
Copy number abnormalities in human cancer from comparative genomic hybridization experiments
database
summary
proGenomes
Fullam, Anthony; Letunic, Ivica,; Schmidt, Thomas S; Ducarmon, Quinten R.; Karcher, Nicolai; Khedkar, Supriya; Kuhn, Michael; Larralde, Martin; Maistrenko, Oleksandr; Malfertheiner, Lukas; Milanese, Alessio; Rodrigues, Joao Frederico Matias; Sanchis-LÃ³pez
proGenomes3: approaching providing one million accurately and consistently
database
summary
ProGlycProt
Alka Rao
Experimentally characterized Prokaryotic GlycoProteins
database
summary
PROMISCUOUS
Gohlke, BjÃƒÂ¶rn; Gallo, Kathleen; Goede, Andrean; Eckert, Andreas; Moahamed, Barbara; Preissner, Robert
Protein-protein and drug-protein interactions for studies of drug repositioning
database
summary
ProNAB
Gromiha, Michael; Harini, Kannan; Srivastava, Ambuj; Kulandaisamy, Arulsamy
Protein-Nucleic Acid Binding affinity
database
summary
ProOpDB
Enrique Merino
Prokaryotic Operon DataBase
database
summary
ProPan
Xiao, Jingfa; Zhang, Yadong; Zhang, Hao; Zhang, Zaichao; Qian, Qiheng; Zhang, Zhewen
Prokaryotic pan-genomes
database
summary
PROPHECY
Fernandez-Ricaud L.
, Warringer J.
, Ericson E.
, Glaab K.
, Davidsson P.
, Nilsson F
, Kemp G.J.L.
, Nerman O.
and Blomberg A.
Profiling of phenotypic characteristics in yeast
database
summary
ProPortal
Sallie W. Chisholm
Prochlorococcus marinus and its phages
database
summary
ProRepeat
Jack Leunissen
Amino acid tandem Repeats in Proteins
database
summary
ProRule
Sigrist C.J.A.
, Bairoch A.
1,2
, Bulliard V.
, De Castro E.
, Langendijk-Genevaux P.S.
and Hulo N.
Functional and structural information on PROSITE profiles
database
summary
ProSAS
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure
database
summary
PROSITE
Hulo, N., Sigrist, C.J.A., Langendijk-Genevaux, P., Le Saux, V., Bairoch, A.
Biologically-significant protein patterns and profiles
database
summary
PROTAC-DB
Hou, Tingjun; Weng, Gaoqi; Cai, Xuanyan; Cao, Dong-Sheng; Du, Hongyan; Shen, Chao; Deng, Yafeng; He, Qiaojun; Yang, Bo; Li, Dan
PROTAC-DB 2.0: an updated database of PROTACs
database
summary
PROTAC-DB
Hou, Tingjun. (proxy) (contact); Weng, Gaoqi; Shen, Chao; Cao, Dong-Sheng; Gao, Junbo; Dong, Xiaowu; He, Qiaojun; Yang, Bo; Li, Dan.`; Wu, Jian
Proteolysis-targeting chimeras (PROTACs)
database
summary
ProtCAD
Xu, Qifang; Dunbrack, Roland
Protein Common Assembly Database
database
summary
ProtChemSI
Olga Kalinina
Protein-Chemical Structural Interactions
database
summary
ProtCID
Qifang Xu and Roland L. Dunbrack, Jr
Protein Common Interface Database
database
summary
Protegen
Brian Yang
1,2,3
, Samantha Sayers
1,2,4
, Zuoshuang Xiang
1,2,5
and Yongqun He
1,2,5
Protective antigen database and analysis system
database
summary
Protein Clusters
Related protein sequences (clusters)of Reference Sequence proteins encoded by complete genomes
database
summary
Protein Geometry Database
Donald S. Berkholz, Peter B. Krenesky, John R. Davidson, and P. Andrew Karplus
Protein conformation and bond angles and lengths
database
summary
Protein kinase resource
Protein kinase sequences, enzymology, genetics, and molecular and structural properties.
database
summary
Protein Naming Utility
Johannes Goll, Robert Montgomery, Lauren M. Brinkac, Seth Schobel, Derek M. Harkins, Yinong Sebastian, Susmita Shrivastava, Scott Durkin, and Granger Sutton
Repository of protein names and naming rules
database
summary
Protein-protein interfaces
Interacting residues in protein-protein interfaces in PDB
database
summary
Proteome-pI
Kozlowski, Lukasz
Pre-computed isoelectric points for proteomes of >5000 organisms
database
summary
Proteome-pI 2.0
Kozlowski, Lukasz
Proteome-pI 2.0 is an updated version of an online database (Proteome-pI
[h
database
summary
ProteomeScout
Naegle, Kristen; Holehouse, Alex; Matlock, Matthew
Proteomics of post-translational modifications
database
summary
ProteomeXchange
Vizcaino, Juan Antonio; Deutsch, Erik; Csordas, Attila; Sun, Zhi; Jarnuczak, Andrew; Perez-Riverol, Yasset; Ternent, Tobias; Campbell, David S.; Bernal-Llinares, Manuel; Okuda, Shujiro; Kawano, Shin; Moritz, Robert; Carver, Jeremy; Wang, Mingxun; Ishihama, Yasushi; Bandeira, Nuno; Hermjakob, Henning
Proteomics resources portal
database
summary
ProteomeXchange
Vizcaino, Juan Antonio; Deutsch, Erik; Csordas, Attila; Sun, Zhi; Jarnuczak, Andrew; Perez-Riverol, Yasset; Ternent, Tobias; Campbell, David S.; Bernal-Llinares, Manuel; Okuda, Shujiro; Kawano, Shin; Moritz, Robert; Carver, Jeremy; Wang, Mingxun; Ishihama, Yasushi; Bandeira, Nuno; Hermjakob, Henning
Proteomics resources portal
database
summary
ProteomeXchange
Deutsch, Erik; Bandeira, Nuno; Perez-Riverol, Yasset; Sharma, Vagisha; Carver, Jeremy; Kundu, Deepti J.; Wang, Shengbo; Bandla, Chakradhar; Kamatchinathan, Selvakumar; Hewapathirana, Suresh; Pullman, Benjamin; Wertz, Julie; Sun, Zhi.; Kawano, Shin; Okuda,
The ProteomeXchange Consortium at 10 years: 2023 update
database
summary
ProteomicsDB
Tobias Schmidt, Patroklos Samaras, Martin Frejno, Siegfried Gessulat, Maximilian Barnert, Harald Kienegger, Helmut Krcmar, Judith Schleg, Hans-Christian Ehrlich, Stephan Aiche, Bernhard Kuster, Mathias Wilhelm
ProteomicsDB is a joint effort of the Technische UniversitÃƒÂ¤t MÃƒÂ¼nchen (TUM) and SAP SE. It is dedicated to expedite the identification of the human proteome and its use across the scientific community.
database
summary
ProteomicsDB
Wilhelm, Mathias; Lautenbacher, Ludwig; Samaras, Patroklos; Mueller, Julian; Grafberger, Andreas; Shraideh, Marwin; Rank, Johannes; Fuchs, Simon; Schmidt, Tobias K; The, Matthew; Dallago, Christian; Wittges, Holger; Rost, Burkard; Krcmar, Helmut; Kuster,
ProteomicsDB: Towards a FAIR open-source resource for life-science research
database
summary
ProteoNexus
Yang Yang; et al.
ProteoNexus characterizes genetic architecture, estimates mediation effects and drug targets through proteome-wide association study
database
summary
ProTeus
Signature sequences at the protein N- and C-termini
database
summary
ProTherm
Gromiha, Michael; Nikam, Rahul; Kulandaisamy, A.; Harini, K.; Sharma, Divya
Thermodynamic data for wild-type and mutant proteins
database
summary
ProtoNet
Linial, Michal; Rappoport, Nadav; Karsenty, Solange; Stern, Amos; Linial, Nathan
Hierarchical clustering of SWISS-PROT proteins
database
summary
ProtozoaDB
Genome analysis of Plasmodium, Entamoeba, Trypanosoma and Leishmania
database
summary
PRRDB
Lata S. and Raghava G.P.S.
Pattern recognition receptors and their ligands
database
summary
PRTAD
Sun X.
, Di Wu
, Jernigan R.
1,3
, Wu Z.
1,4
Protein Residue Torsion Angle Distributions
database
summary
PSCDB
Takayuki Amemiya
Protein Structural Change upon ligand binding
database
summary
PseudoBase++
Batenburg, F.H.D. van
, Gultyaev, A.P.
, Pleij, C.W.A.
Structural, functional and sequence data related to RNA pseudoknots
database
summary
Pseudofam
Eukaryotic pseudogenes assigned to different protein families
database
summary
PseudoGene
Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P. and Gerstein M.
Pseudogenes in eukaryotic and prokaryotic genomes
database
summary
Pseudomonas Genome Database
Brinkman, F. and Geoff Winsor, G.
Pseudomonas
genome database and community annotation project
database
summary
PSI-SGKB
Protein Structure Initiative Structural Genomics Knowledgebase
database
summary
PSORTdb
Brinkman, Fiona; Lau, Wing Yin Venus; Hoad, Gemma L; Jin, Vivian; Winsor, Geoffrey; Madyan, Ashmeet; Gray, Kristen; Laird, Matthew R; Lo, Raymond
Protein subcellular localization in bacteria
database
summary
PSSRdb
Pankaj Kumar, Pasumarthy S. Chaitanya, and Hampapathalu A. Nagarajaram
Polymorphic Simple Sequence Repeats Database
database
summary
PTGL
Patrick May, Annika Kreuchwig, Thomas Steinke, and Ina Koch
Protein Topology Graph library: Secondary structure-based protein topologies
database
summary
PTMcode
Peer Bork
Functional associations between posttranslational modifications within proteins
database
summary
PubAngioGen
Yi, Zhengfang; Li, Peng; Liu, Yongrui; Wang, Huan; He, Yuan; Wang, Xue; He, Yundong; Lv, Fang; Chen, Huaqing; Pang, Xiufeng; Liu, Mingyao; Shi, Tieliu
Public angiogenesis research portal
database
summary
PubChem
Bolton, Evan; Kim, Sunghwan; Chen, Jie'; Cheng, Tiejun; Gindulyte, Asta; He, Jane; He, Siqian; Li, Qingliang.; Shoemaker, Benjamin; Thiessen, Paul; Yu, Bo.; Zaslavsky, Leonid; Zhang, Jian
Structures and biological activities of small organic molecules
database
summary
Pubchem
Kim, Sunghwan; Chen, Jie'; Cheng, Tiejun; Gindulyte, Asta; He, Jane; He, Siqian; Li, Qingliang.; Shoemaker, Benjamin; Thiessen, Paul; Yu, Bo.; Zaslavsky, Leonid; Zhang, Jian!; Bolton, Evan
PubChem 2023 update
database
summary
PubMed
Citations and abstracts of biomedical literature
database
summary
PULDB
Terrapon, Nicolas; Lombard, Vincent; Drula, Elodie; LapÃ©bie, Pascal; Al-Masaudi, Saad; Gilbert, Harry; Henrissat, Bernard
No description supplied
database
summary
pVOGs
Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen
Prokaryotic Virus Orthgologous Groups
database
summary
PWAS
Michal Linial
Proteome-Wide Association Studies
database
summary
PyIgClassify
Dunbrack, Roland; Adolf-Bryfogle, Jared; Xu, Qifang; North, Benjamin; Lehmann, Andreas
Clusters of conformations of antibody CDRs
database
summary
qPrimerDB
Lu, Kun; LI, Tian; He, Jian; Chang, Wei; Zhang, Rui`,; Liu, Miao; Yu, Mengna; Fan, Yonghai; Sun, Wei``; Ma, Jinqi; Qu, Cunmin; Liu, Liezhao; Li, Nannan; Liang, Yin; Wang, Rui; Tang, Zhanglin; Qian, Wei; Xu, Xinfu; Lei, Bo; Zhang, Kai; Li, Jiana
Real-time quantitative polymerase chain reaction (qPCR) is one of the most
database
summary
qPrimerDepot
Quantitative real time PCR primers for human and mouse RefSeq sequences
database
summary
qPTM
Liu, Zexian; Yu, Kai; Wang, Ye; Zheng, Yongqiang; Liu, Zekun; Zhang, Qingfeng2; Wang, Siyu; Zhao, Qi ,; Zhang, Xiaolong; Li, Xiaoxing; Xu, Rui-Hua
Quantitative Post-Translational Modifications
database
summary
qPTMplants
Cheng, Han; Xue, Han; Zhang, Qingfeng2; Wang, Panqin; Cao, Bijin; Jia, Chongchong; Cheng, Ben; Shi, Yuhua; Guo, Wei-Feng; Wang, Zhenlong; Liu, Ze-Xian
Plant PTMs, including quantitation
database
summary
QSproteome
Edward Catoiu; et al.
QSproteome: A Community-Driven Interactive Platform for Scalable Exploration of Quorum Sensing Proteomes
database
summary
QTL Matchmaker
Star K.V.
1,2
, Song Q.
, Zhu A.
and BÃƒÆ’Ã‚Â¶ttinger E.P.
Quantitative trait loci information for human, mouse and rat
database
summary
QTLbase
Li, Mulin Jun; Huang, Dandan; Feng, Xiangling; Yang, Hongxi; Wang, Jianhua; Zhang, Wenwen; Fan, Xutong; Chen, Kexin; Yu, Ying``; Yi, Xianfu; Ma, Xin; Dong, Xiaobao
QTLbase2: an enhanced catalog of human quantitative trait loci on extensive
database
summary
QUADRAtlas
Dassi, Erik; Bourdon, SÃ©bastien; Dumas, LeÃ¯la; Herviou, Pauline; Destefanis, Eliana; Zen, Andrea; Cammas, Anne; millevoi, stefania
RNA G-Quadruplex and RG4-binding proteins
database
summary
QUADRatlas
bourdon, SÃ©bastien; Herviou, Pauline; Dumas, LeÃ¯la; Destefanis, Eliana; Zen, Andrea; Cammas, Anne; Millevoi, Stefania; Dassi, Erik
QUADRatlas is the RNA G-quadruplex and RG4-binding proteins database.
database
summary
Quorumpeps
Bart De Spiegeleer
A database of quorum-sensing peptides
database
summary
R-loopBase
Chen, Jia-Yu; Lin, Ruoyao; Zhong, Xiaoming; Zhou, Yongli; Geng, Huichao; Hu, Qingxi; Huang, Zhihao; Hu, Jun; Fu, Xiang-Dong; Chen, Liang
R-loops and R-loop regulators
database
summary
R-LoopDB
Kuznetsov, Vladimir; Jenjaroenpun, Piroon; Wongsurawat, Thidathip; Sutheeworapong, Sawannee
R-loop forming sequences
database
summary
R.E.DD.B.
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments
database
summary
RABC
Chen, Haiyan; Xu, Jing,; Wei, Siyu; Jia, Zhe; Sun, Chen; Kang, Jingxuan; Guo, Xuying; Zhang, Nan; Tao, Junxian; Dong, Yu; Zhang, Chen; Ma, Yingnan; Lv, Wenhua; Tian, Hongsheng; Bi, Shuo; Lv, Hongchao; Huang, Chen; Kong, Fanwu; Tang, Guoping; Jiang, Yongsh
Multi-omics of Rheumatoid Arthritis
database
summary
RACe
Yihao Chen; et al.
RACe: a database for rare cancer clinical and molecular associations
database
summary
RADAR
Ramaswami, Gokul; Li, Jin Billy
A Rigorously Annotated Database of A-to-I RNA editing
database
summary
RadioPharm
Feng Zhu; et al.
RadioPharm: the database of radiopharmaceuticals (RPs)
database
summary
RaftProt
Shah, Anup; Chen, David; Boda, Akash; Foster, Leonard; Davis, Melissa; Hill, Michelle M
Lipid raft associated proteins in mammals
database
summary
RAID
Wang, Dong; Yi, Ying; Zhao, Yue; Li, Chunhua; Zhang, Lin.,; Huang, Huiying; Li, YaNa; Liu, Lanlan; Hou, Ping; Cui, Tianyu; Tan, Puwen; Hu, Yongfei; Zhang, Ting'.; Huang, Yan.; li, xiaobo; Yu, Jia
Human RNA-RNA and RNA-protein interactions
database
summary
RAP-DB
Ohyanagi H.
1,2
, Tanaka T.
, Sakai H.
, Shigemoto Y.
1,4
, Yamaguchi K.
, Habara T.
5,6
, Fujii Y.
5,6
, Antonio B.A.
, Nagamura Y.
, Imanishi T.
, Ikeo K.
, Itoh T.
3,6
, Gojobori T.
1,6
and Sasaki T.
The Rice Annotation Project database
database
summary
RAPID
Resource of Asian Primary Immunodeficiency Diseases
database
summary
RARGE - RIKEN Arabidopsis Genome Encyclopedia
Arabidopsis
cDNAs, mutants and microarray data
database
summary
RASP
Yuhan Fei
RNA secondary structure probing data
database
summary
RAVAR
Cao, Chen; Shao, Mengting; Zuo, Chunman; Kwok, Devin; Liu, Lin; Ge, Yuli; Zhang, Zilong; Cui, Feifei; Chen, Mingshuai; Fan, Rui; Ding, Yijie; Jiang, Hangjin; Wang, Guishen; Zou, Quan.
RAVAR: a curated repository for rare variant-trait associations
database
summary
RBP-Var
Sun, Zhongsheng; Mao, Fengbiao; Xiao, Luoyuan; Li, Xianfeng; Teng, Huajing.; Cai, Wanshi
Human genome variants which could change the RNA structure and affect RNA-protein interactions
database
summary
RBP2GO
Caudron-Herger, Maiwen; Jansen, Ralf; Wassmer, Elsa; Diederichs, Sven
RNA-binding proteins across species
database
summary
RBPDB
Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, and Timothy R. Hughes
RNA-binding proteins and their specificities
database
summary
RBPimage
Benoit Bouvrette, Louis Philip; Wang, Xiaofeng; Boulais, Jonathan; Kong, Jian; Uddin Syed, Easin; Blue, Steven; Zhan, Lijun; Olson, Sara; Stanton, Rebecca; Wei, Xintao; Yee, Brian; Van Nostrand, Eric; Fu, Xiang-Dong; Burge, Chris; Graveley, Brenton R.; Ye
Microscopy reporting subcellular distribution of human RNA binding proteins
database
summary
RCSB
Stephen Burley; et al.
RCSB Protein Data Bank: Delivering Integrative Structures Alongside Experimentally Determined ones
database
summary
RCSB
Burley, Stephen; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chao, Henry; Chen, Li; Craig, Paul A.; Crichlow, Gregg; Dalenberg, Kenneth; Duarte, Jose; Dutta, Shuchismita; Fayazi, Maryam; Feng, Zukang; Flatt, Justin W.; Ganesan, Sai; Ghosh, Sutap
RCSB Protein Data Bank (RCSB.org): Delivery of Experimentally-Determined PD
database
summary
RCSB Protein Data Bank
Burley, Stephen; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chen, Li,`; Crichlow, Gregg; Christie, Cole; Dalenberg, Kenneth; Di Costanzo, Luigi; Duarte, Jose; Dutta, Shuchismita; Feng, Zukang; Ganesan, Sai; Goodsell, David; Ghosh, Sutapa; Krame
All biological macromolecular structures
database
summary
RDBSB
Wan Liu
Registry and Database of Bioparts for Synthetic Biology
database
summary
Reactome
D'Eustachio, Peter G; Gillespie, Marc; Jassal, Bijay; Stephen, Ralf; Milacic, Marija; Rothfels, Karen; Senff-Ribeiro, Andrea; Griss, Johannes; Sevilla, Cristoffer; Matthews, Lisa; Gong, Chuqiao; Deng, Chuan; Varusai, Thawfeek; Ragueneau, Eliot; Haider, Yu
The Reactome Pathway Knowledgebase 2022
database
summary
Reactome
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
A database of metabolic and signaling pathways
database
summary
Reactome
D'Eustachio, Peter G; Milacic, Marija; Beavers, Deidre; Conley, Patrickinactive; Gong, Chuqiao; Gillespie, Marc; Griss, Johannes; Haw, Robin; Jassal, Bijay; Matthews, Lisa; May, Bruce; Petryszak, Robert; Ragueneau, Eliot; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Stephen, Ralf; Tiwari, Krishna; Varusai, Thawfeek; Weiser, Joel; Wu, Guanming; Stein, Lincoln.; Hermjakob, Henning
The Reactome Knowledgebase (https://reactome.org) provides molecular detail
database
summary
REBASE
Roberts, Rich; Posfai, Janos; Vincze, Tamas; Macelis, Dana
Restriction enzymes and associated methylases
database
summary
REBASE
Roberts, Richard; Vincze, Tamas; Posfai, Janos; Macelis, Dana
REBASE - A Database for DNA Restriction and Modification: Enzymes, Genes an
database
summary
REDfly
Regulatory modules and transcription factor binding sites in Drosophila
database
summary
REDIportal
Picardi, Ernesto; Mansi, Luigi; Tangaro, Marco Antonio; Lo Giudice, Claudio; Flati, Tiziano; Kopel, Eli; Schaffer, Amos; CastrignanÃƒÂ², Tiziana; Chillemi, Giovanni; Pesole, Graziano
A-to-I RNA editing events in human
database
summary
RefMetaPlant
Li, Xuan; Shi, Han; Wu, Xueting; Zhu, Yan; Jiang, Tao; Wang, Zhengwei; Li, Xuetong; Liu, Jianju; Zhang, YIngxue; Chen, Feng; Gao, Jinshan; Xu, Xiaoyan; Zhang, Guo-Qing; Xiao, Ning; Feng, Xianzhong; Zhang, Peng; Wu, Yongrui; Hu, Yonghong; Li, Aihong; Chen, Ping
RefMetaPlant: a reference metabolome database for plants across five major phyla
database
summary
REFOLD
Buckle A.M.
Experimental data on protein refolding and purification
database
summary
RefSeq
Thibaud-Nissen, Francoise; Haft, Daniel H.; Badretdin, Azat; Coulouris, George; DiCuccio, Michael; Durkin, A; Jovenitti, Eric; Li, Wenjun; Mersha, Megdelawit; O'Neill, Kathleen; Virothaisakun, Joel
The Reference Sequence (RefSeq) project at the National Center for Biotechn
database
summary
RefSeq (microbial)
Tatusova, Tatiana (proxy); Ciufo, Stacy; Federhen, Scott; Fedorov, Boris; McVeigh, Richard; O'Neill, Kathleen; Zaslavsky, Leonid
The National Center for Biotechnology Information Reference Sequence (RefSe
database
summary
Regeneration Roadmap
Liu, Guang-Hui; Kang, Wang; Jin, Tong; Zhang, Tao .; Ma, Shuai; Yan, Haoteng; LIU, ZUNPENG; Ji, Zhejun; Cai, Yusheng; Wang, Si; SONG, Moshi; REN, JIE; Zhou, Qi; qu, jing; ZHANG, WEIQI; Bao, Yi-Ming
Literature and multi-omics data on cell regeneration
database
summary
RegPhos
Tzong-Yi Lee
, Justin Bo-Kai Hsu
, Wen-Chi Chang
and Hsien-Da Huang
2,4,5
Regulatory Network in Protein Phosphorylation
database
summary
RegPrecise
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov
Predicted regulons in prokaryotic genomes
database
summary
RegTransBase
Kazakov A.E.
, Cipriano M.J.
, Novichkov P.S.
3,4
, Minovitsky S.
, Vinogradov D.V.
, Arkin A.
2,4,5,6
, Mironov A.A.
1,7,8
, Gelfand M.S.
1,7,8,10
, Dubchak I.
2,9,10
Manually curated database of regulatory interactions in prokaryotes
database
summary
RegulonDB
Collado-Vides, Julio; Salgado, Heladia; Gama-Castro, Socorro; Mejia-Almonte, Citlalli; Lara, Paloma; AlarcÃ³n-Carranza, Gabriel; LÃ³pez-Almazo, AndrÃ©s G.; Betancourt-Figueroa, Felipe; PeÃ±a-Loredo, Pablo; Alquicira-HernÃ¡ndez, Shirley; Ledezma-Tejeida, Daniel
RegulonDB 12.0: Key transformative improvements in the modeling and conceptualization of transcriptional regulation in E. coli K-12
database
summary
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12
Santos-Zavaleta, Alberto;Salgado, Heladia;Gama-Castro, Socorro;SÃƒÂ¡nchez-PÃƒÂ©rez, Mishael;GÃƒÂ³mez-Romero, Laura;Ledezma-Tejeida, Daniela;GarcÃƒÂa-Sotelo, Jair Santiago;Alquicira-HernÃƒÂ¡ndez, Kevin;MuÃƒÂ±iz-Rascado, Luis JosÃƒÂ©;PeÃƒÂ±a-Loredo, Pablo;Ishida-GutiÃƒÂ©rrez, Cecilia;VelÃƒÂ¡zquez-RamÃƒÂrez, David A;DelÃ‚Â Moral-ChÃƒÂ¡vez, VÃƒÂctor;Bonavides-MartÃƒÂnez, CÃƒÂ©sar;MÃƒÂ©ndez-Cruz, Carlos-Francisco;Galagan, James;Collado-Vides, Julio
No description supplied
database
summary
ReMap
Ballester, Benoit; ChÃƒÂ¨neby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony
With this latest release of ReMap (http://remap.cisreg.eu), we present a un
database
summary
ReMap
Ballester, Benoit; Hammal, Fayrouz; de Langen, Pierre; Bergon, AurÃ©lie; Lopez, Fabrice
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulato
database
summary
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
ChÃƒÂ¨neby, Jeanne;MÃƒÂ©nÃƒÂ©trier, Zacharie;Mestdagh, Martin;Rosnet, Thomas;Douida, Allyssa;Rhalloussi, Wassim;Bergon, AurÃƒÂ©lie;Lopez, Fabrice;Ballester, Benoit
No description supplied
database
summary
REPAIRtoire
Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosi?ski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osi?ska, Kristian Rother, and Janusz M. Bujnicki
DNA repair pathways of human, yeast and E.coli
database
summary
RepeatsDB
Tosatto, Silvio; Paladin, Lisanna; Bevilacqua, Martina; Errigo, Sara; Piovesan, Damiano; MiÃ„\x8DetiÃ„â€¡, Ivan; Necci, Marco; Monzon, Alexander; Fabre, Maria Laura; Lopez, Jose Luis; Nilsson, Juliet; Rios, Javier; Lorenzano Menna, Pablo; Cabrera, Maia; Gonzalez B
Repeats in protein structures
database
summary
ReplicationDomain (alias ChromosomeDomain)
Weddington, N., Stuy, A., Hiratani, I., Ryba, T., Yokochi, T., and Gilbert, D.M.
ReplicationDomain: Replication timing database and genome-wide data visualization tool. ChromosomeDomain: database of any chromosome features tied to a map unit.
database
summary
RepoDB
Adam S. Brown & Chirag J. Patel
Drug repositioning, the process of discovering, validating, and marketing p
database
summary
RepTar
Naama Elefant, Amnon Berger, Harel Shein, Matan Hofree, Hanah Margalit, and Yael Altuvia
Predicted targets of host and viral miRNAs
database
summary
RESID
Protein structure modifications
database
summary
ResMicroDB
Mingkun Li; et al.
ResMicroDB: A comprehensive database and analysis platform for human microbiome resistance
database
summary
RetNet
Lori S Sullivan, Sara J Bowne, Stephen P. Daiger
RetNet provides tables of genes and loci causing inherited retinal diseases
database
summary
RetroRules
Duigou, Thomas; et al.
RetroRules: a database of reaction rules for metabolic engineering and synthetic biology
database
summary
RetrOryza
Chaparro C.
, Guyot R.
, Zuccolo A.
2,
PiÃƒÂ©gu B.
and Panaud O.
LTR-retrotransposons in rice
database
summary
Rfam
Nawrocki, Eric; Burge, Sarah W; Bateman, Alex; Daub, Jennifer; Eberhardt, Ruth; Eddy, Sean; Floden, Evan; Gardner, Paul; Jones, Thomas; Tate, John; Finn, Robert
No description supplied
database
summary
Rfam
Petrov, Anton; Kalvari, Ioanna; Nawrocki, Eric; Ontiveros-Palacios, Nancy; Argasinska, Joanna; Lamkiewicz, Kevin; Marz, Manja; Griffiths-Jones, Sam; Toffano-Nioche, Claire; Gautheret, Daniel; Weinberg, Zasha; Rivas, Elena; Eddy, Sean R; Finn, Robert; Bateman, Alex
No description supplied
database
summary
RGD
Jiang, Yu; Fu, Weiwei; Wang, Rui; Asadollahpour Nanaei, Hojjat; Wang, Jinxin; Hu, Dexiang
Ruminant Genome Database
database
summary
Rhea
Bridge, Alan J; Bansal, Parit; Morgat, Anne; Axelsen, Kristian; Muthukrishnan, Venkatesh; Coudert, Elisabeth; Aimo, Lucila; Hyka-Nouspikel, Nevila; Gasteiger, Elisabeth; Kerhornou, Arnaud; Neto, Teresa; Pozzato, Monica; Blatter, Marie-Claude; Ignatchenko,
Rhea, the reaction knowledgebase in 2022
database
summary
Rhea
Morgat, Anne; Axelsen, Kristian; Lombardot, Thierry; AlcÃƒÂ¡ntara, Rafael; Aimo, Lucila; Zerara, Mohamed; Niknejad, Anne; Belda, Eugeni; Hyka-Nouspikel, Nevila; Coudert, Elisabeth; Redaschi, Nicole; Bougueleret, Lydie; Steinbeck, Christoph; Xenarios, Ioannis; Bridge, Alan
Expert-curated biochemical reactions
database
summary
RhesusBase
Shi-Jian Zhang
1,#
, Chu-Jun Liu
1,#
, Mingming Shi
1,#
, Lei Kong
, Jia-Yu Chen
, Wei-Zhen Zhou
, Xiaotong Zhu
, Peng Yu
, Jue Wang
, Xinzhuan Yang
, Ning Hou
, Zhiqiang Ye
, Rongli Zhang
, Ruiping Xiao
, Xiuqin Zhang
1,*
and Chuan-Yun Li
1,*
A Knowledgebase for the Monkey Research Community
database
summary
Ribo_uORF
Liu, Qi .; Peng, Xin; Mengyuan, Shen; Qian, Qian; Xing, Junlian; Gregory, Richard
uORFs from ribosome profiling data [MAKE MICRO]
database
summary
Ribocentre
Huang, Lin; Deng, Jie; Shi, Yaohuang; Peng, Xuemei; He, Yuanlin; Chen, Xiaoxue; Li, Mengxiao; Lin, Xiaowei; Liao, Wenjian; Huang, Yuanyin; Jiang, Taijiao; Lilley, David; Miao, Zhichao
Ribozymes
database
summary
Ribocentre-aptamers
Zhichao Miao; et al.
Ribocentre-aptamers: An integrative, Structure-Focused Database for RNA Aptamers
database
summary
Ribocentre-switch
Huang, Lin; Bu, Fan; Lin, Xiaowei; Liao, Wenjian; Lu, Zhizhong; He, Yuanlin; Luo, Yuhang; Peng, Xuemei; Li, Mengxiao; Huang, Yuanyin; Chen, Xiaoxue; Xiao, Bowen; Jiang, Jiuhong; Deng, Jie; Huang, Jian; Lin, Tianxin; Miao, Zhichao
Ribocentre-switch: A database of riboswitches
database
summary
Ribonuclease P Database
RNase P sequences, alignments, and structures
database
summary
Ribosomal Database Project (RDP-II)
Cole, J.R.
, Chai, B.
, Wang, Q.
, Chandra, S.
, Farris, R.J.
, Kulam, S.A.
, McGarrel, D.M.
, Schmidt, T.M.
, Garrity, G.M.
, Tiedje, J.M.
rRNA sequence data, analysis tools, alignments, and phylogenies
database
summary
RiboXYZ
DAO DUC, KHANH; Kushner, Artem; Petrov, Anton S.
Ribosome structures
database
summary
Rice Annotation Database
Contig data for manual annotation of rice genome
database
summary
Rice Gene Thresher
Web-based Application for Mining Genes Underlying QTLs in Rice Genome
database
summary
Rice Mutant Database
Rice mutant database
database
summary
Rice Pipeline
Unification tool for rice databases
database
summary
Rice Proteome Database
Rice proteome database
database
summary
RiceFREND
Baltazar Antonio
Rice Functionally Related gene Expression Network Database
database
summary
RiceGAAS
Sakata K., Nagamura Y., Numa H., Antonio B.A., Nagasaki H., Idonuma A., Watanabe W., Shimizu Y., Horiuchi I., Matsumoto T., Sasaki T. and Higo K.
Rice genome automated annotation system
database
summary
RiceVarMap
Xie, Weibo; hu, zhao; Yao, Wen; Ouyang, Yidan; Yang, Wanneng; Wang, Gongwei; Lian, Xingming; Xing, Yongzhong; Chen, Ling-ling .
Rice Variation Map, SNPs and indels
database
summary
RiceXPro
Yutaka Sato, Baltazar A. Antonio, Nobukazu Namiki, Hinako Takehisa, Hiroshi Minami, Kaori Kamatsuki, Kazuhiko Sugimoto, Yuji Shimizu, Hirohiko Hirochika, and Yoshiaki Nagamura
Rice transcriptome under natural conditions
database
summary
RIDOM - Ribosomal Differentiation of Medical Microorganisms
Harmsen, D.
, RothgÃƒÂ¤nger, J.
, Sammeth, M.
, Albert, J.
rRNA (16S and ITS) sequence-based identification of medical microorganisms
database
summary
RIKEN mammals
Integrated database of mammalian genomes, phenotypes, strains and cell lines
database
summary
RISE
Zhang, Qiangfeng; Gong, Jing; Shao, Di; Xu, Kui; Lu, Zhipeng; Lu, Zhi; Yang, Yu-Cheng
No description supplied
database
summary
RJunBase
Huang, Shenglin; Li, Qin; Lai, Hongyan; Li, Yuchen; Chen, Bing..; Li, Yan ..; Huang, Zhaohui; Meng, Zhiqiang; Wang, Peng5; hu, zhixiang
RNA splice junctions
database
summary
RLBase
Bishop, Alexander; Miller, Henry; Montemayor, Daniel; Li, Janet; Levy, Simon; Pawar, Roshan; Hartono, Stella; Sharma, Kumar; Frost, Bess; ChÃ©din, FrÃ©dÃ©ric
R-loops in the human genome
database
summary
RM2Target
Bao, Xiaoqiong; Zhang, Yin; Li, Huiqin; Teng, Yuyan; Ma, Lixia; Chen, Zhihang; Zheng, Jian.; Zhao, An; Ren, Jian.; Zuo, Zhixiang
Targets of RNA modification proteins
database
summary
RMBase
Yang, Jian-Hua; Xuan, Jia-Jia; Sun, Wen-Ju; Lin, Peng-Hui; Zhou, Ke-Ren; Liu, Shun; Zheng, Ling-Ling; Qu, Liang-Hu
No description supplied
database
summary
RMBase
Yang, Jian-Hua; Sun, Wen-Ju; Li, Jun-Hao; Liu, Shun; Wu, Jie .; Zhou, Hui`'; Qu, Liang-Hu
RNA Modification DataBase
database
summary
RMBase
Yang, Jian-Hua ; Xuan, Jia-Jia; Chen, Lifan; Chen, Zhirong; Huang, Junhong; Lin, Jinran; Zheng, Lingling; Li, Bin; Qu, Liang-Hu
RMBase v3.0: Decode the Landscape, Mechanisms and Functions of RNA Modifications
database
summary
RMDB
Das, Rhiju; Yesselman, Joseph; Tian, Siqi; Liu, Xin; Shi, Lei; Li, Jin Billy
No description supplied
database
summary
RMdisease
Song, Bowen; Wang, Xuan; Liang, Zhanmin; Ma, Jiongming; huang, daiyun; Wang, Yue; de MagalhÃ£es, JoÃ£o Pedro; Rigden, Daniel J.; Meng, Jia; Liu, Gang; Chen, Kunqi; Wei, Zhen
RMDisease V2.0: an updated database of genetic variants that affect RNA mod
database
summary
RMDisease
Chen, Kunqi; Song, Bowen; Tang, Yujiao; Wei, Zhen.; Xu, Qingru; MagalhÃƒÂ£es, JoÃƒÂ£o Pedro de; Su, Jionglong; Meng, Jia; Rigden, Daniel J.
Genetic variants that affect RNA modifications vs disease
database
summary
RMPore
Ming-shi Zhixiang; et al.
RMPore: a comprehensive database of single-molecule RNA modifications
database
summary
RMVar
Zuo, Zhixiang; Luo, Xiaotong; Li, Huiqin; Liang, Jiaqi; Zhao, Qi ,; Xie, Yubin; Ren, Jian
Genetic variants that affect RNA modifications vs disease
database
summary
RNA Bricks
Chojnowski, Grzegorz; Walen, Tomasz; Bujnicki, Janusz
RNA structural modules and their interactions
database
summary
RNA CoSSMos
Pamela Vanegas
RNA Characterization of Secondary Structure Motifs
database
summary
RNA FRABASE
A database of 3D RNA fragments within known RNA structures
database
summary
RNA Modification Database
Naturally modified nucleosides in RNA
database
summary
RNA Mutation Database
Triman K.L.
16S and 23S ribosomal RNA mutations
database
summary
RNA SSTRAND
RNA secondary structure data and structural motifs
database
summary
RNAcentral
Bateman, Alex
Data for non-protein coding RNA genes
database
summary
RNAdb
Pang K.C.
1,2
, Stephen S.
, EngstrÖm P.G.
, Tajul-Arifin K.
, Chen W.
, Wahlestedt C.
, Lenhard B.
, Hayashizaki Y.
, and Mattick J.S.
Mammalian noncoding RNA database
database
summary
RNAdisease
Wang, Dong; Chen, Jia; Lin, jiahao; Hu, Yongfei; Ye, Meijun; Yao, Linhui; Wu, Le; Zhang, Wenhai; Wang, Meiyi; Deng, Tingting; Huang, Yan; Zhu, Bofeng
RNADisease v4.0: an updated resource of RNA-associated diseases, providing
database
summary
RNAi codex
Olson A., Sheth N., Lee J.S., Hannon G. and Sachidanandam R.
Available clones from mouse, human and rat shRNA libraries
database
summary
RNAiDB
RNAi phenotypic analysis of C. elegans genes
database
summary
RNAInter
Wang, Dong; Kang, Juanjuan; Tang, Qiang; He, Jun; Li, Le; Yang, Nianling; Yu, Shuiyan; Wang, Mengyao; Zhang, Yuchen; Lin, Jiahao; Cheng, Jun; Cui, Tianyu; Su, Xi; Huang, Yan; Chen, Wei
RNAInter v4.0: RNA interactome repository with redefined confidence scoring
database
summary
RNAInter in 2020: RNA interactome repository with increased coverage and annotation
Lin, Yunqing;Liu, Tianyuan;Cui, Tianyu;Wang, Zhao;Zhang, Yuncong;Tan, Puwen;Huang, Yan;Yu, Jia;Wang, Dong
No description supplied
database
summary
RNAJunction
RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions
database
summary
RNALocate
Wang, Dong; Lin, Hao ,; Li, Kongning; Zhang, Ting; Tan, Puwen; Wang, Liqiang; Jin, Nana; Li, YaNa; Zhang, Lin.,; Yang, Huan; Hu, Zhenyu; Zhang, LiNing; Hu, Chunyu; Li, Chunhua; Qian, Kun; Zhang, Changjian; Huang, Yan.
RNA Localization in the cell
database
summary
RNALocate
Wang, Dong; Cui, Tianyu; Dou, Yiying; Tan, Puwen; Ni, Zhen; Liu, Tianyuan; Wang, Duolin; Huang, Yan; Cai, Kaican; Zhao, Xiaoyang; Lin, Hao; Xu, Dong,
RNALocate v2.0: an updated resource for RNA subcellular localization with i
database
summary
RNApaceDB
Shuyuan Wang; et al.
RNApaceDB: a dedicated database to dissect RNA velocity across diverse biological contexts
database
summary
RNApathwaysDB
Janusz Bujnicki
A database of RNA processing pathways
database
summary
RNAPhaSep
Wang, Dong; Zhu, Haibo; Fu, Hao; Cui, Tianyu; Ning, Lin; Shao, Huaguo; Guo, Yehan; Ke, Yanting; Zheng, Jiayi; Lin, Hongyan; Wu, Xin; Liu, Guanghao; He, Jun; Han, Xin; Li, Wenlin; Zhao, Xiaoyang; Shen, Xiaopei; Hu, Kongfa
RNAs involved in liquid-liquid phase separation
database
summary
RNArchitecture
Bujnicki, Janusz M.; Boccaletto, Pietro; Magnus, Marcin; Almeida, Catarina; Zyla, Adriana; Astha, Astha; Pluta, Radoslaw; Baginski, Blazej; Jankowska, Elzbieta; Dunin-Horkawicz, Stanislaw; Wirecki, Tomasz; Boniecki, Michal; Stefaniak, Filip
RNArchitecture is a database that provides a comprehensive description of r
database
summary
RNRdb
Lundin D., Torrents E., Furrer E., Larsson Birgander P., Sahlin M., Poole A.M. and SjÃƒÆ’Ã‚Â¶berg B.-M.
Ribonucleotide reductase database
database
summary
RodentGMPOmics Atlas
Shuo Su
Rodent Genome and Pathogen Microbiome Database
database
summary
rOGED
Gieske, M.C., Payne, C.E., Gieske, J.B., and CheMyong Ko
Rat ovarian gene expression database
database
summary
RPFdb
Xie, Zhi; Xie, Shang-Qian; Nie, Peng; Wang, Yan`; Wang, Hongwei,; Li, Hongyu; Yang, Zhilong; Ren, Jian
Ribosome profiling database
database
summary
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling
Wang, Hongwei;Yang, Ludong;Wang, Yan;Chen, Leshi;Li, Huihui;Xie, Zhi
No description supplied
database
summary
RPG - Ribosomal Protein Gene database
Ribosomal protein gene database
database
summary
RPS
Zuo, Zhixiang; Liu, Mengni; Li, Huiqin; Luo, Xiaotong; Cai, Jieyi; Chen, Tianjian; Xie, Yubin; Ren, Jian.
RNAs involved in liquid-liquid phase separation
database
summary
RsiteDB
RNA-binding sites database
database
summary
rSNPBase 3.0
Wang, Jing; Guo, Liyuan
No description supplied
database
summary
rVarbase
Wang, Jing; Guo, Liyuan; Du, Yang; Qu, Susu
Annotated SNPs within regulatory DNA elements
database
summary
RVdb
Zhao, Peng; Liu, Bo `; Su, Haoxiang; Han, Yelin; Xu, Panpan; Zhou, Siyu,; Hu, Yongfeng; Wu, Zhiqiang; Dong, Jie; Sui, Hongtao; Li, Xin; Yang, Jian,,; Zhang, Ting; Yang, Fan15
RVdb: A Comprehensive Database and Integrated Analysis Platform for Rhinovirus Research
database
summary
S/MARt DB
Liebich I.
and Wingender E.
1,2
Nuclear scaffold/matrix attached regions
database
summary
SAbDab
Schneider, Constantin; Raybould, Matthew; Deane, Charlotte
SAbDab-nano: A comprehensive and continuously updated database of nanobody
database
summary
SAbDab
Deane, Charlotte; Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terence; Fuchs, Angelika; Georges, Guy; Shi, Jiye
Structural Antibody Database
database
summary
SABIO-RK
Ulrike Wittig
System for the Analysis of Biochemical Pathways Reaction Kinetics
database
summary
SABIO-RK
Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Kania, Renate; MÃƒÂ¼ller, Wolfgang
No description supplied
database
summary
SAGEmap
NCBI's resource for SAGE data from various organisms
database
summary
SAHG
Structural Atlas of Human Genome
database
summary
SARS-CoV RNA SSS
Wei-Bo Liu
Predicted secondary structures of SARS coronavirus RNA
database
summary
SASBDB
Svergun, Dmitri; Valentini, Erica; Kikhney, Alexey; Previtali, Gianpietro; Jeffries, Cy
Small Angle Scattering Biological Data Bank
database
summary
SATPdb
Singh, Sandeep; Chaudhary, Kumardeep; Dhanda, Sandeep; Bhalla, Sherry; Usmani, Salman; Gautam, Ankur; Tuknait, Abhishek; Agrawal, Piyush; Mathur, Deepika; Raghava, Gajendra
A database of structurally annotated peptides
database
summary
SBASE
Vlahovicek, K
, Kajan, L
, ÃƒÆ’Ã‚\x81goston, V
, Pongor, S
Protein domain sequences and tools
database
summary
SBCCDB
Mann, Karen; Newberg, Justin; Mann, Michael; Jenkins, Nancy; Copeland, Neal
No description supplied
database
summary
SBR-Blood
Lichtenberg, Jens; Heuston, Elisabeth; Mishra, Tejaswini; Keller, Cheryl; Hardison, Ross; Bodine, David
Expression and epigenetic data for mouse hematopoietic cell types
database
summary
sc-PDB
Desaphy, JÃƒÂ©rÃƒÂ©my; Bret, Guillaume; Rognan, Didier; Kellenberger, Esther
Potential drug-binding sites in protein structures from the PDB
database
summary
SC2disease
zhao, tianyi; Lyu, Shuxuan; Lu, Guilin; Juan, Liran; Zeng, Xi; hao, jianye; Peng, Jiajie; wei, zhongyu
Single cell transcriptomics data and disease
database
summary
sc2GWAS
Chunquan Li
Relationships between GWAS traits and individual cells
database
summary
SCAN
Chen, Dongsheng; Deng, Yushan; Lu, Yubao; Li, Mengrou; Shen, Jiayi; Qin, Siying; Zhang, Wei; Zhang, Qiang; Shen, Zhaoyang; Li, Changxiao; Jia, Tengfei; Chen, Peixin; Peng, Lingmin; Chen, Yangfeng; Zhang, Wensheng; Liu, Hebin; Zhang, Liangming; Rong, Limin; Wang, Xiangdong
SCAN: Spatiotemporal Cloud Atlas for Neural cells
database
summary
scAPAatlas
Yang, Yang; Yang, Xiaoxiao; Tong, Yang; Liu, Gerui; Yuan, Jiapei
scRNAseq-based analysis of alternative polyadenylation across cells, tissues and species
database
summary
scAPAdb
Wu, Xiaohui; Zhu, Sheng; Lian, Qiwei; Ye, Wenbin; Qin, Wei; Wu, Zhe; Ji, Guoli
scRNAseq-based analysis of alternative polyadenylation across cells, tissues and species
database
summary
SCAR
Chen, Dongsheng; Deng, Yushan; Xiao, Jiedan; Chen, Peixin; Li, Mengrou; Shen, Jiayi; Jia, Tengfei; Li, Changxiao; Chang, Ashley; Zhang, Wensheng; Liu, Hebin; Xue, Ruidong; Zhang, Ning; Wang, Xiangdong; Huang, Li
SCAR: Single-cell and Spatially-resolved CAncer Resources
database
summary
scATAC-Ref
Li, Chunquan; Qian, Feng-Cui; Zhou, Liwei; Zhu, Yanbing; Li, Yanyu; Yu, Zhengmin; Feng, Chenchen; Zhao, Yu3; Fang, Qiaoli; cai, fuhong; Wang, Qiuyu
scRef: a reference of scATAC-seq with known cell labels in multi-species
database
summary
scCancerExplorer
Shuhui Bian
Single-cell multi-omics data of human cancer
database
summary
scCT-DB
Zhongyang Liu; et al.
scCT-DB, an omnicbus for cancer patient-derived paired pre- and post-treatment single-cell transcriptome atlas
database
summary
scDrugAct
Feng Li
Single-cell Drug Action Atlas
database
summary
scEnhancer
Gao, Tianshun; Zheng, Zilong; Pan, Yihang; Zhu, Chengming; Wei, Fuxin; Yuan, Jinqiu; Sun, Rui; Fang, Shuo; Wang, Nan; Zhou, Yang; Qian, Jiang
Single-cell enhancer resource
database
summary
ScerTF
Aaron Spivak
Binding sites for Saccharomyces cerevisiae Transcription Factors
database
summary
scGeneBank
Xiangdong Wang; et al.
scGeneBank: cross-species screening of functional gene sets at single-cell resolution
database
summary
scGRNbase
Li, Chunquan; Huang, Xuemei; Song, Chao; Zhang, Guorui; Li, Ye; Zhao, Yu3; Zhang, Qinyi; Zhang, Yuexin2; Fan, Shifan; Zhao, Jun2
scGRNbase: a comprehensive single-cell gene regulatory network database of human and mouse
database
summary
SchistoDB
Zerlotini, A.
1,2
, Heiges, M.
, Wang, H.
, Moraes, R.L.V.
, Dominitini, A.J.
, Ruiz, J.C.
, Kissinger, J.C.
2,3
Oliveira, G.
Schistosoma mansoni genome resource
database
summary
Sci-ModoM
Christoph Dieterich
Transcriptome-wide high-throughput RNA modification sites
database
summary
scImmOmics
Chunqan Li
Single-cell multi-omics immune database
database
summary
scLTdb
Weike Pei
Single-cell lineage tracing database
database
summary
SCMD - Saccharomyces cerevisiae Morphological Database
Saito T.L.
1,3
, Nakatani Y.
1,3
, Sese J.
, Sano F.
2,3
, Yukawa M.
2,3
, Ohya Y.
2,3
and Morishita S.
1,3
Micrographs of budding yeast mutants
database
summary
scMethBank
Bao, Yi-Ming; Wenting, Zong; Hongen, Kang; Xiong, Zhuang; Ma, Yingke; Jin, Tong; Gong, Zheng; Lizhi, Yi; Zhang, Mochen; Song, Wu; Guoliang, Wang; Li, Rujiao
Single Cell methylation data
database
summary
scMMO-atlas
Wenfei Jin
Single-cell multimodal omics
database
summary
scMOVIR
Zhixiang Zuo; et al.
scMOVIR: a single-cell multi-omics database for human viral infections
database
summary
SCOP2 - Structural Classification Of Proteins
Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha and Alexey G. Murzin
Structural classification of proteins
database
summary
SCOPe
Chandonia, John-Marc; Guan, Lindsey; Lin, Shiangyi; Yu, Changhua; Fox, Naomi; Brenner, Steven
SCOPe: Improvements to the Structural Classification of Proteins â€“ extend
database
summary
SCOPe
Fox, Naomi; Brenner, Steven; Chandonia, John-Marc
Sequences of domains of known structure, selected subsets, and sequence-structure correspondences
database
summary
SCOPPI
Winter, C., Henschel, A., Kim W.K., Schroeder, M.
Structural classification of protein-protein interfaces
database
summary
SCoV2-MD
Selent, Jana; Torrens-Fontanals, Mariona; Peralta GarcÃa, Alejandro; Talarico, Carmine; GuixÃ -GonzÃ¡lez, Ramon; Giorgino, Toni
Molecular dynamics of SARS-Cov-2 proteins and variant interpretation
database
summary
SCovid
Cheng, Liang; Qi, Changlu; Wang, Chao; Zhao, Lingling; Zhu, Zijun; Wang, Ping; Zhang, Sainan; Zhang, Xue1
Single cell transcriptomics of SARS-CoV-2 infection
database
summary
scPlantDB
Chen, Dijun; He, Zhaohui; Luo, Yuting; Zhou, Xinkai; Zhu, Tao; Lan, Yangming
scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases
database
summary
SCPortalen
Kasukawa, Takeya; Abugessaisa, Imad; Noguchi, Shuhei; BÃƒÂ¶ttcher, Michael; Hasegawa, Akira; Kouno, Tsukasa; Kato, Sachi; Tada, Yuhki; Ura, Hiroki; Abe, Kuniya; Shin, Jay; Plessy, Charles; Carninci, Piero
Published single-cell datasets are rich resources for investigators who wan
database
summary
scProAtlas
Xiaobo Zhou
Single-cell spatial proteomics imaging in human tissues
database
summary
scQTLbase
Li, Lei; Ding, Ruofan; Wang, Qixuan; Gong, Lihai; Zhang, Ting; Zou, Xudong; Xiong, Kewei; Liao, Qi; Plass, Mireya
scQTLbase: an integrated human single-cell eQTL database
database
summary
ScRAPdb
Jia-Xing Yue
Saccharomyces cerevisiae reference assembly panel
database
summary
SCRIPDB
Abraham Heifets
Search for Chemicals and Reactions In Patents
database
summary
scTEA-db [CHECK]
Gruber, Andreas; Barquin, Miguel; Kouzel, Ian; Ehrmann, Beat; Basler, Michael
scTEA-db: A comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes
database
summary
scTML
Xuegong Zhang
Single-cell tumor mutation landscape
database
summary
scTWASAtlas
Jingfa Xiao
Single-cell transcriptome-wide association studies
database
summary
scVMAP
Chunquan Li; et al.
scVMAP: a comprehensive platform for integrating single-cell chromatin accessibility and gene expression maps
database
summary
SDAP
Ivanciuc, O., Schein, C.H., Braun, W.
Sequences, structures, and IgE epitopes of allergenic proteins
database
summary
SDMap
Yanjun Xu; et al.
SDMap: a comprehensive database of spatial drug perturbation map
database
summary
SEA
Zhang, Yan; Wei, Yanjun; Zhang, Shumei; Shang, Shipeng; Zhang, Bin; Li, Song .; Wang, Xinyu; Wang, Fang `; Su, Jianzhong; Wu, Qion g; Liu, Hongbo
A database of super enhancers
database
summary
SEA version 3.0:Ã‚Â a comprehensive extension and update of the Super-Enhancer archive
Chen, Chuangeng;Zhou, Dianshuang;Gu, Yue;Wang, Cong;Zhang, Mengyan;Lin, Xiangyu;Xing, Jie;Wang, Hongli;Zhang, Yan
No description supplied
database
summary
SEAweb: the small RNA Expression Atlas web application
Rahman, Raza-Ur;Liebhoff, Anna-Maria;Bansal, Vikas;Fiosins, Maksims;Rajput, Ashish;Sattar, Abdul;Magruder, Daniel S;Madan, Sumit;Sun, Ting;Gautam, Abhivyakti;Heins, Sven;Liwinski, Timur;Bethune, JÃƒÂ¶rn;Trenkwalder, Claudia;Fluck, Juliane;Mollenhauer, Brit;Bonn, Stefan
No description supplied
database
summary
Sebida
Sex bias in insect gene expression database
database
summary
SecReT4
Dexi Bi
, Linmeng Liu
, Cui Tai
, Zixin Deng
, Kumar Rajakumar
, Hong-Yu Ou
SecReT4: a web-based bacterial type IV secretion system resource
database
summary
Secreted Protein Database
Secreted proteins from human, mouse and rat
database
summary
SEdb
Wang, Yuezhu; Song, Chao; Zhao, Jun; Zhang, Yuexin; Zhao, Xilong; Feng, Chenchen; Zhang, Guorui; Zhu, Jiang6; Wang, Fan,; Qian, Feng-Cui; Zhou, Liwei; Zhang, Jian.,; Ai, Bo; Liu, Xinyu; Wang, Qiuyu; Li, Chunquan
SEdb 2.0: a comprehensive super-enhancer database of human and mouse
database
summary
SEdb: a comprehensive human super-enhancer database
Jiang, Yong;Qian, Fengcui;Bai, Xuefeng;Liu, Yuejuan;Wang, Qiuyu;Ai, Bo;Han, Xiaole;Shi, Shanshan;Zhang, Jian;Li, Xuecang;Tang, Zhidong;Pan, Qi;Wang, Yuezhu;Wang, Fan;Li, Chunquan
No description supplied
database
summary
SEECancer
Li, Xia; Zhang, Hongyi; Luo, Shangyi; Zhang, Xinxin .; Liao, Jianlong; Quan, Fei; Zhao, Erjie; Zhou, Chenfen; Yu, Fulong; Zhang, Yunpeng; Xiao, Yun
No description supplied
database
summary
SeedGenes
Genes essential for Arabidopsis development
database
summary
SeekPCMDB
Peilin Jia; et al.
SeekPCMDB: knowledge on disease-associated protein-coding mutations
database
summary
Selectome
Robinson-Rechavi, Marc; Moretti, Sebastien; Laurenczy, Balazs; Gharib, Walid; Castella, Briseis; Kuzniar, Arnold; Schabauer, Hannes; Studer, Romain; Valle, Mario; Salamin, Nicolas; Stockinger, Heinz
Gene trees that show positive selection
database
summary
SelenoDB
RomagnÃƒÆ’Ã‚Â©, FrÃƒÆ’Ã‚Â©dÃƒÆ’Ã‚Â©ric; Santesmasses, Didac; White, Louise; Sarangi, Gaurab; Mariotti, Marco; HÃƒÆ’Ã‚Â¼bler, Ron; Weihmann, Antje; Parra, Genis; Gladyshev, Vadim; GuigÃƒÆ’Ã‚Â³, Roderic; Castellano, Sergi
A database of selenoprotein genes, proteins and SECIS elements
database
summary
SELEXdb
Selected DNA/RNA functional site sequences
database
summary
SelTarbase
Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, and Peer Bork
Mutations of human MSI-H tumor and colorectal cell lines
database
summary
SENTRA
Michael Galperin
A census of SENsory signal TRAnsduction proteins
database
summary
SEQanswers
Dan Bolser
Wiki on all aspects of next-generation genomics
database
summary
SEVA
de Lorenzo, Victor; Martinez-Garcia, Esteban; Aparicio, Tomas; Goni, Angel; Fraile, Sofia
The Standard European Vector Architecture: a platform for analysis of complex prokaryotic phenotypes
database
summary
SEVA
de Lorenzo, Victor; Martinez-Garcia, Esteban; Fraile, Sofia; Algar Parejo, Elena; Aparicio, Tomas; VelÃ¡zquez MuÃ±oz, Elena; Calles, Belen; TAS, HUSEYIN; BlÃ¡zquez, Blas; Martin, Bruno; Prieto HernÃ¡ndez, Clara; SÃ¡nchez-Sampedro, Lucas; NÃ¸rholm, Morten; Volke
SEVA 4.0: an update of the Standard European Vector Architecture database f
database
summary
SEVENS
Suwa, M.
, Sato, T.
, Okouchi, I.
, Arita, M.
, Matsumoto, S.
, Tsutsumi, S.
, Aburatani, H.
, Asai, K.
, Akiya, Y.
7-transmembrane helix receptors
database
summary
SFLD
Babbitt, Patricia; Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel; Barber, Alan; Custer, Ashley; Hicks, Michael; Huang, Conrad; Lauck, Florian; Mashiyama, Susan; Meng, Elaine; Mischel, David; Morris, John; Schnoes, Alexandra; Stryke, Doug; Yunes, Jeffrey; Ferrin, Thomas; Holliday, Gemma
Structure-Function Linkage Database
database
summary
SGD
Cherry, J. Michael; Skrzypek, Marek; Nash, Rob; Wong, Edith; MacPherson, Kevin; Hellerstedt, Sage; Engel, Stacia; Karra, Kalpana; Weng, Shuai; Sheppard, Travis; Binkley, Gail; Simison, Matt; Miyasato, Stuart
No description supplied
database
summary
SGD -
Saccharomyces
Genome Database
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.
Saccharomyces cerevisiae
genes, gene products and their annotations.
database
summary
Shanghai Rapeseed Database
Seed development and fatty acid metabolism of oilseed crops
database
summary
SIB resources
Mendes de Farias, Tarcisio; Zahn-Zabal, Monique; Bolleman, Jerven; Altenhoff, Adrian; Bairoch, Amos; Bansal, Parit; Baratin, Delphine; Bastian, Frederic; Bridge, Alan J; Burdet, Frederic; Crameri, Katrin; Dauvillier, Jerome; Dessimoz, Christophe; Gehant, Sebastien; Glover, Natasha; Gnodtke, Kristin; Hayes, Catherine; Ibberson, Mark; Kriventseva, Evgenia; Kuznetsov, Dmitry; Lisacek, Frederique; Mehl, Florence; Michel, Pierre-Andre; Moretti, Sebastien; Morgat, Anne; Oesterle, Sabine; Pagni, Marco; Redaschi, Nicole; Robinson-Rechavi, Marc; Samarasinghe, Kasun; Sima, Ana-Claudia; Szklarczyk, Damian; Topalov, Orlin; Toure, Vasundra; Unni, Deepak; Von Mering, Christian; Wollbrett, Julien; Zdobnov, Evgeny
The SIB Swiss Institute of Bioinformatics is a federation of bioinformatics
database
summary
SIDDBase
Wang H., Kaloper M. and Benham C.J.
Stress-induced DNA duplex destabilization profiles of complete microbial genomes
database
summary
SIDER
Bork, Peer; Kuhn, Michael; Letunic, Ivica; Jensen, Lars,
Side Effect Resource: adverse drug reactions
database
summary
SIFTS
support@ebi.ac.uk
Structure Integration with Function, Taxonomy and Sequences
database
summary
SigMol
Kumar, Manoj; Rajput, Akanksha; Kaur, Karambir
Experimentally validated Quorum sensing signaling molecules (QSSMs) in prokaryotes
database
summary
SignaLink
Csabai, Luca; Fazekas, DÃ¡vid; Kadlecsik, TamÃ¡s; Szalay-BekÅ‘, MÃ¡tÃ©; BohÃ¡r, BalÃ¡zs; Madgwick, Matthew; MÃ³dos, DezsÅ‘; Ã–lbei, MÃ¡rton; Gul, Lejla; Sudhakar, Padhmanand; Kubisch, JÃ¡nos; Oyeyemi, Oyebode James; Liska, Orsolya; Ari, Eszter; Hotzi, Bernadette; Billes, Viktor A.; MolnÃ¡r, Eszter; FÃ¶ldvÃ¡ri-Nagy, LÃ¡szlÃ³; CsÃ¡lyi, Kitti; Demeter, Amanda; PÃ¡pai, NÃ³ra; Koltai, MihÃ¡ly; Varga, MÃ¡tÃ©; Lenti, Katalin; Farkas, IllÃ©s J; TÃ¼rei, DÃ©nes; Csermely, PÃ©ter; Vellai, Tibor; KorcsmÃ¡ros, TamÃ¡s
Tissue-specific signaling networks in model organisms
database
summary
SIGNOR
Perfetto, Livia; Lo Surdo, Prisca; Iannuccelli, Marta; Licata, Luana; Contino, Silvia; Castagnoli, Luisa; Cesareni, Gianni
SIGNOR 3.0, the SIGnaling Network Open Resource 3.0: 2022 update
database
summary
SIGNOR
Cesareni, Gianni; Perfetto, Livia; Briganti, Leonardo; Calderone, Alberto; Cerquone Perpetuini, Andrea; Iannuccelli, Marta; Langone, Francesca; Licata, Luana; Marinkovic, Milica; Mattioni, Anna; Pavlidou, Theodora; Peluso, Daniele; Petrilli, Lucia; PirrÃƒÂ², Stefano; Posca, Daniela; Santonico, Elena; Silvestri, Alessandra; Spada, Filomena; Castagnoli, Luisa
SIGnaling Network Open Resource
database
summary
SilencerDB
Jiang, Rui; Zeng, Wanwen; Chen, Shengquan; Cui, Xuejian; Chen, Xiaoyang; Gao, Zijing
Human silencers, validated or predicted
database
summary
SilkMeta
Dai, Fangyin; Lu, Kunpeng; Pan, Yifei; Shen, Jianghong; Yang, Lin; Zhan, Chengyu; Liang, Shubo; Tai, Shuaishuai; Wan, Linrong; LI, Tian.; Cheng, Tingcai; Ma, Bi; Pan, Guoqing; He, Ningjia; Lu, Cheng; Westhof, Eric; Xiang, Zhonghuai; Han, Min-Jin; Tong, Xiaoling
SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data
database
summary
SilkSatDb
Prasad, M.D.
, Muthulakshmi, M.
, Arunkumar, K.P.
, Madhu, M.1, Sreenu, V.B.
, Pavithra, V.
, Bose, B.
, Nagarajaram, H.A.
, Mita, K.
, Shimada, T.
and Nagaraju, J.
A microsatellite database of the silkworm
Bombyx mori
database
summary
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data
Yilmaz, Pelin; Wegener Parfrey, Laura; Yarza, Pablo; Gerken, Jan; PrÃƒÆ’Ã‚Â¼sse, Elmar; Quast, Christian; Schweer, Timmy; Peplies, JÃƒÆ’Ã‚Â¶rg; Ludwig, Wolfgang; GlÃƒÆ’Ã‚Â¶ckner, Frank Oliver
The SILVA (from Latin silva, forest) databases provides comprehensive, quality checked and regularly updated databases of aligned small- (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature.
database
summary
SIMAP
Rattei, Thomas; Arnold, Roland,; Goldenberg, Florian; Mewes, Hans-Werner
Pre-calculated protein sequence similarities, domains, annotations and clusters
database
summary
SINEBase
Dmitri Kramerov
A database of short interspersed elements (SINEs)
database
summary
SingPro
Han, Lianyi; LIAN, Xichen; ZHANG, Yintao; ZHOU, Ying; Sun, Xiuna; HUANG, Shijie; Zhu, Feng
SCPRDB: a knowledge base providing single-cell proteomic data
database
summary
siRecords
Experimentally tested mammalian siRNAs
database
summary
siRNAdb
Warfinge R.E., Chalk A.M. and Sonnhammer E.L.L.
Functional human siRNA sequences
database
summary
SISYPHUS
Andreeva A.
, Prlic A.
, Hubbard T.J.P.
and Murzin A.G.
Structural alignments for proteins with non-trivial relationships
database
summary
SitEx
Irina Medvedeva
Projections of protein functional Sites on Exons
database
summary
SKY/M-FISH and CGH
Fluorescent images of chromosomes and cytogenetic data
database
summary
SLKB
Li, Lang; GÃ¶kbaÄŸ, Birkan; Tang, Shan; Fan, Kunjie; Cheng, Lijun; Yu, Lianbo; Zhao, Yue
SLKB: Synthetic lethality knowledge base
database
summary
smallBARNA
Shusruto Rishik; et al.
SmallBARNA 2026: A Kingdom-wide bacterial small RNA resource
database
summary
SMART
Bork, Peer; Letunic, Ivica; Khedkar, Supriya
Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
database
summary
SMART
Bork, Peer; Letunic, Ivica
SMART (Simple Modular Architecture Research Tool) is a web resource (http:/
database
summary
SMC
Daniel Udwary
Secondary Metabolism Collaboratory
database
summary
SmedGD
The Schmidtea mediterranea genome database
database
summary
SMMRNA
Parkesh, Raman; Mehta, Ankita; Sonam, Surabhi; Gouri, Isha; Loharch, Saurabh; Sharma, Deepak K
Small molecule inhibitors of RNA
database
summary
SMoS.2: Update of database of Structural Motifs in Superfamilies
Anita Rachel Chacko, Oommen K. Mathew, Adwait Joshi, Upadhyayula Surya Raghavender and R. Sowdhamini
Open Data Drug & Drug Target Database
database
summary
SMPDB
Wishart, David; Jewison, Tim; Su, Yilu; Miri Disfany, Fatemeh; Liang, Jack; Knox, Craig; Maciejewski, Adam; Poelzer, Jenna; Huynh, Jessica; Zhu, You; Arndt, David; Djoumbou, Yannick; Liu, Yifeng; Deng, Lu; Guo, An Chi; Han, Beomsoo; Pon, Allison; Wilson, Michael.; Rafatnia, Shahrzad; Liu, Philip
Small Molecule Pathway Database
database
summary
SNAPPI
Jefferson E.R., Walsh T., Roberts T. and Barton, G.J.
Structures, iNterfaces and Alignments for Protein-Protein Interactions
database
summary
Sno/scaRNAbase
Xie J.
, Zhang M.
, Zhou T.
, Hua X.
, Tang L.S.
and Wu W.L.
Small nucleolar RNAs and cajal body-specific RNAs
database
summary
snoDB
Scott, Michelle; Bergeron, Danny; Paraqindes, Hermes; Fafard-Couture, Etienne; Deschamps-Francoeur, Gabrielle; Faucher Giguere, Laurence; Bouchard-Bourelle, Philia; Abou Elela, Sherif; Catez, FrÃ©dÃ©ric; Marcel, Virginie
snoDB 2.0: An enhanced interactive database, specializing in human snoRNAs
database
summary
snoDB: an interactive database of human snoRNA sequences, abundance and interactions
Bouchard-Bourelle, Philia;Desjardins-Henri, ClÃƒÂ©ment;Mathurin-St-Pierre, Darren;Deschamps-Francoeur, Gabrielle;Fafard-Couture, Ãƒâ€°tienne;Garant, Jean-Michel;Elela, Sherif Abou;Scott, Michelle S
No description supplied
database
summary
snOPY
Yoshihama M, Nakao A, Kenmochi N.
No description supplied
database
summary
snoRNA-LBME-db
Lestrade L.
and Weber M.J.
Human snoRNAs and Cajal body-specific RNAs (scaRNAs)
database
summary
SNP-Seek
Alexandrov, Nickolai; Mansueto, Locedie; Palis, Kevin; Fuentes, Roven; Ulat, Victor; Chebotarov, Dmytro; Tai, Shuaishuai; Zhang, Gengyun; Li, Zhikang; Mauleon, Ramil; Hamilton, Ruaraidh; McNally, Kenneth
Rice SNPs from 3,000 rice genomes
database
summary
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers
Yang, Yanbo;Zhang, Qiong;Miao, Ya-Ru;Yang, Jiajun;Yang, Wenqian;Yu, Fangda;Wang, Dongyang;Guo, An-Yuan;Gong, Jing
No description supplied
database
summary
SNP2TFBS
Bucher, Philipp; Ambrosini, Giovanna; Kumar, Sunil
Regulatory SNPs affecting predicted transcription factor binding sites
database
summary
SNP500Cancer
Re-sequenced SNPs from 102 reference samples
database
summary
SNPedia
Greg Lennon
Wiki on SNPs and genome annotation
database
summary
SNPeffect
De Baets, Greet
1,2,3
; Van Durme, Joost
1,2,3
; Reumers, Joke
4,5
; Maurer-Stroh, Sebastian
; Vanhee, Peter
1,3
; Dopazo, Joaquin
7,8
; Schymkowitz, Joost
1,2
and Rousseau, Frederic
1,2
Phenotypic effects of human coding SNPs
database
summary
SNPlogic
Interactive SNP annotation, selection and prioritization system for genotyping projects and/or analysis and interpretation of SNP data.
database
summary
SNPSTR
Microsatellite compound markers in 5 vertebrate genomes
database
summary
So3D
Li Wang; et al.
So3D: a comprehensive three-dimensional spatial omics resource for decoding the molecular spatial architecture of tissues
database
summary
SoIR
Qing-Yong Yang
Solanaceae information resource
database
summary
SolGenomics
Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.; Saha, Surya,; Tecle, Isaak; Strickler, Susan; Bombarely, Aureliano; York, Thomas; Pujar, Anuradha; Foerster, Hartmut; Yan, Aimin; Mueller, Lukas
Solanaceae Genomics Network
database
summary
SomamiR
Yan Cui
Somatic mutations that impact microRNA targeting in cancer
database
summary
SomaMutDB
Sun, Shixiang; Wang, Yujue; Maslov, Alexander; Dong, Xiao; Vijg, Jan
Somatic mutations in normal human tissues
database
summary
SORC
Xu, Juan; Zhou, Weiwei; Su, Minghai; Jiang, Tiantongfei; Yang, Qingyi; Sun, Qisen; Xu, Kang1; Shi, Jingyi; Yang, Changbo; Ding, Na; Li, Yongsheng
SORC: An Integrated Spatial Omics Resource in Cancer
database
summary
sORFs
Olexiouk, Volodimir; Menschaert, Gerben; CrappÃƒÂ©, Jeroen; Verbruggen, Steven
Small ORFs identified by ribosome profiling
database
summary
sORFs.org
Olexiouk, Volodimir; Van Criekinge, Wim; Menschaert, Gerben
No description supplied
database
summary
SOURCE
Diehn, M.
, Sherlock, G.
, Binkley, G.
, Jin, H.
, Hernandez-Boussard, T.
, Cherry, J.M.
, Brown, P.O.
, Alizadeh, A.A.
Functional genomic resource for annotations, ontologies, and expression data
database
summary
SoyBase
Nelson, Rex; Brown, Anne; Conners, Shawn; Huang, Wei; Wilkey, Andrew; Grant, David; Weeks, Nathan; Cannon, Steven; Graham, Michelle
Soybean genetics and genomics
database
summary
SoyKB - Soybean Knowledge Base
Joshi, T.
1,2,3,4
, Fitzpatrick, M.R.
1,2
, Chen, S.
1,2
, Liu, Y.
2,4
, Zhang, H.
1,2
, Endacott, R.Z.
1,2
, Gaudiello, E.C.
1,2
, Stacey, G.
2,3,5
, Nguyen, H.T.
2,3,5
, Xu, D.
1,2,3,4
Soybean Knowledge Base
database
summary
SoyMD
Fang, Chao; Yang, Zhiquan; Luo, Chengfang; Pei, Xinxin; Wang, Shengbo; Huang, Yiming; Li, Jiawei; Liu, Baohui; Kong, Fanjiang; Yang, Qing-Yong
SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding
database
summary
SoyNet
Kim, Eiru; Hwang, Sohyun; Lee, Insuk
Co-functional networks for soy bean, Glycine max
database
summary
SPASCER
Fan, Zhiwei; Luo, Yangyang; Lu, Huifen; Wang, Tiangang; Feng, Yuzhou; Zhao, Weiling; Kim, Pora; Zhou, Xiaobo1
Spatial transcriptomics annotation at single-cell resolution
database
summary
SPathDB
Yanjun Xu
Heterogeneity of functional activity from spatial transcriptomics
database
summary
Spatial GWAS Atlas
Yajie Zhao; et al.
Spatial GWAS Atlas: a knowledgebase for decoding the genetic architecture of spatial gene expression
database
summary
Spatial2GWAS
Pora Kim; et al.
Spatial2GWAS: a database for linking spatial transcriptomic regions with GWAS variants and disease traits
database
summary
SpatialDB: a database for spatially resolved transcriptomes
Fan, Zhen;Chen, Runsheng;Chen, Xiaowei
Spatially resolved transcriptomic techniques allow the characterization of
database
summary
SpatialRef
Chunqan Li
Manually curated spatial omics
database
summary
SpBase
Sea urchin Strongylocentrotus purpuratus genome database
database
summary
SPDB
Wang, Guohua; Wang, Fang; Liu, Chunpu; Li, Jiawei; Yang, Fan; Song, Jiangning; Yao, Jianhua
SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution
database
summary
SPEED
Chen, Yangfeng; Zhang, Xingliang; Peng, Xi; Jin, Yicheng; Ding, Peiwen; Xiao, Jiedan; Li, Changxiao; Chang, Ashley; Yue, Qizhen; Pu, Mingyi; Chen, Peixin; Shen, Jiayi; Li, Mengrou; Jia, Tengfei; Wang, Haoyu; Huang, Li; Guo, Guoji; Zhang, Wensheng .; Liu,
Single-cell pan-species atlas
database
summary
SPEED
Searchable prototype experimental evolutionary database
database
summary
SPENCER
Xie, Yubin; Luo, Xiaotong; Huang, Yuantai; Li, Huiqin; Luo, Yihai; Zuo, Zhixiang; Ren, Jian.
Cancer-associated ncRNA-encoded small peptides
database
summary
SpermatogenesisOnline
Qinghua Shi
Spermatogenesis-related genes
database
summary
SPICA
Carmona, Santiago; Andreatta, Massimo; David, Fabrice; Iseli, Christian; Guex, Nicolas
Swiss Portal for Immune Cell Analysis
database
summary
SPIKE
Arnon Paz, Zippora Brownstein, Yaara Ber, Shani Bialik, Eyal David, Dorit Sagir, Igor Ulitsky, Ran Elkon, Adi Kimchi, Karen B. Avraham, Yosef Shiloh, and Ron Shamir
Signaling Pathways Integrated Knowledge Engine
database
summary
SPIRE
Schmidt, Thomas S; Fullam, Anthony; Ferretti, Pamela; Orakov, Askarbek; Maistrenko, Oleksandr; Ruscheweyh, Hans; Duan, Yiqian; Van Rossum, Thea; Sunagawa, Shinichi; Mende, Daniel R; Coelho, Luis Pedro; Bork, Peer
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
database
summary
SpliceAid-F
Graziano Pesole
Human splicing factors and their RNA binding sites
database
summary
SpliceDisease
Juan Wang
Links between RNA splicing and disease
database
summary
SpliceInfo
Modes of alternative splicing in human genome
database
summary
SpliceNest
A tool for visualizing splicing of genes from EST data
database
summary
Spliceosome Database
Melissa Jurica
No description supplied
database
summary
SpodoBase
Genomics of the butterfly
Spodoptera frugiperda
database
summary
SporeWeb
Eijlander, Robyn; de Jong, Anne; Krawczyk, Antonina; Holsappel, Siger; Kuipers, Oscar
Regulatory pathways during the sporulation cycle of Bacillus subtilis
database
summary
SPROUTS
Structural Prediction for pRotein fOlding UTility System
database
summary
SRA
Katz, Ken; Shutov, Oleg; Lapoint, Richard; Kimelman, Michael; Brister, J.; Christopher, O'Sullivan
Sequence Read Archive
database
summary
sRNAMap
small regulatory RNA in microbial genomes
database
summary
sRNATarBase
Jiang Wang
, Tao Liu
, Bo Zhao
, Qixuan Lu
, Zheng Wang
, Yuan Cao
, Wuju Li
Bacterial sRNAs are a class of small regulatory RNAs of about 40 Ã¢â‚¬â€œ 5
database
summary
SRPDB
Alm Rosenblad, M.
, Zwieb, C.
, Samuelsson, T.
Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments
database
summary
SSBD
Onami, Shuichi; Kyoda, Koji; Itoga, Hiroya; Yamagata, Yuki; Fujisawa, Emi; Miranda-Miranda, Miguel; Yamamoto, Haruna; Tohsato, Yukako
Public repository and added-value database for bioimaging data
database
summary
SSRome
Morad M. Mokhtar and Mohamed A. M. Atia
SSRome is a fully functional, comprehensive, integrated database and pipeli
database
summary
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms
Mokhtar, Morad M;Atia, Mohamed AÃ‚Â M
No description supplied
database
summary
SSToSS - Sequence-Structural Templates of Single-member Superfamilies
Chakrabarti, S.
, Manohari, G.
and R. Sowdhamini
Signal recognition particle RNA, SRP protein, and SRP receptor sequences and alignments
database
summary
STAB
Liting Song, Shaojun Pan, Zichao Zhang, Longhao Jia, Wei-Hua Chen, and Xing-Ming Zhao
Spatio-Temporal Cell Atlas of the Human Brain
database
summary
STAB
Zhao, Xing-Ming; Yang, Yucheng T.; Gan, ziquan; Zhang, Jinglong; Zhao, Xingzhong; Yang, Yifan; Han, Shuwen; Wu, Wei
STAB2: an updated Spatio-Temporal cell Atlas of the human and mouse Brain
database
summary
Stanford Tissue Microarray Database
Stanford Tissue Microarray Database
database
summary
STAP refinement of NMRdb
Jinhyuk Lee
Refined solution NMR structures
database
summary
StarBASE
Li, Jun-Hao; Liu, Shun; Zhou, Hui`'; Qu, Liang-Hu; Yang, Jian-Hua
microRNA-mRNA interaction maps
database
summary
Start2Fold
Vranken, Wim; Pancsa, Rita; Varadi, Mihaly; Tompa, Peter
Hydrogen/deuterium exchange data on protein folding and stability
database
summary
STCDB - Signal Transduction Classification Database
Ming Chen, Susana Lin, Ralf Hofestaedt
Signal transductions classification
database
summary
STCRDab
Deane, Charlotte; Leem, Jinwoo; de Oliveira, Saulo; Krawczyk, Konrad
No description supplied
database
summary
StellaBase
Nematostella vectensis
genomics database
database
summary
Stem Cell Discovery Engine
Winston Hide
Comparison system for cancer stem cell analysis
database
summary
StemDriver
Zhou, Xiaobo1; Guo, Jingjing; Liu, Yang; Kim, Pora; Luo, Yangyang; Wen, Jianguo; Zhao, Weiling; Huang, Kexin
StemDriverï¼ša knowledgebase of gene functions for hematopoietic stem cell fate determination
database
summary
STEMFORMATICS
Choi, Jarny; Pacheco, Chris M; Mosbergen, Rowland; Korn, Othmar; Chen, Tyrone; Nagpal, Isha; Englart, Steve; Angel, Paul W; Wells, Christine A;
Stemformatics is an established gene expression data portal containing over
database
summary
StemMapper
Pinto, JosÃƒÂ©; Machado, Rui; Magno, Ramiro; Oliveira, Daniel; Machado, Susana; Andrade, Raquel; BraganÃƒÂ§a, JosÃƒÂ©; Duarte, Isabel; Futschik, Matthias
No description supplied
database
summary
STIFDB2
Mahantesha Naika
1,2
, Khader Shameer
2,3
, Oommen K. Mathew
, Ramanjini Gowda
and R. Sowdhamini
2*
STIFDB2: Stress responsive TrancrIption Factor DataBase version 2
database
summary
STINGreport
Amino acid properties in proteinns of known structure
database
summary
STITCH
Kuhn, Michael; Szklarczyk, Damian; Pletscher-Frankild, Sune; Blicher, Thomas; von Mering, Christian; Jensen, Lars,; Bork, Peer
Search Tool for Interactions of Chemicals
database
summary
STOmicsDB
Ma, Kailong; Xu, Zhicheng; Wang, Weiwen; Yang, Tao; Chen, Jing; Huang, Yan; Gould, Joshua; Du, Wensi; Yang, Fan7; Li, Ling; Hua, cong; Hu, shoujie; Cai, jia; You, lijin; Zeng, wenjun; Wang, bo; Liu, Longqi; Xu, Xun; Chen, Fengzhen; Wei, Xiaofeng; Ma, xizheng; Wang, jieyu; Lu, huifang; li, zhiyong; hu, qingjiang; liu, yiqun; Zhang, Yong13; Li, Yuxiang; Chen, Ao
STOmicsDB: a database of Spatial Transcriptomic data
database
summary
StrainInfo.net Bioportal
Virtual catalogue providing integrated downstream information on microorganisms deposited within a global network of biological resource centers.
database
summary
Strepto_DB
Database for comparative genome analysis of 15 strains of the genus Streptococcus
database
summary
StreptomeDB
Guenther, Stefan; Moumbock, AurÃƒÂ©lien A. F.; Gao, Mingjie; Qaseem, Ammar; Li, Jianyu; Kirchner, Pascal A.; Ndingkokhar, Bakoh; Bekono, Boris D.; Simoben, Conrad V.; Babiaka, Smith B.; Malange, Yvette I.; Sauter, Florian; Zierep, Paul; Ntie-Kang, Fidele
No description supplied
database
summary
STRING
Szklarczyk, Damian; Kirsch, Rebecca; Koutrouli, Mikaela; Nastou, Katerina; Mehryary, Farrokh; Hachilif, Radja; Gable, Annika; FANG, TAO; Doncheva, Nadezhda; Pyysalo, Sampo`; Bork, Peer; Jensen, Lars,; von Mering, Christian
The STRING database in 2023: proteinâ€“protein association networks and fun
database
summary
STRING
von Mering, Christian; Szklarczyk, Damian; Gable, Annika; Nastou, Katerina; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo`; Doncheva, Nadezhda; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars
Predicted functional associations between proteins
database
summary
Structure Superposition Database
Pairwise superposition of TIM-barrel structures
database
summary
stSNV
Tingting Shao
Spatial SNVs in human
database
summary
SUBA
Heazlewood, J.L., Verboom, R.E., Tonti-Filippini, J., Small, I. and Millar, A.H.
Subcellular localisation of
Arabidopsis
proteins
database
summary
SubCELL
Yu Zong Chen
Subcellular compartment-specific interactions
database
summary
SubtiWiki
StÃ¼lke, JÃ¶rg; Pedreira, Tiago; Elfmann, Christoph
The current state of SubtiWiki, the database for the model organism Bacillu
database
summary
SubtiWiki
StÃƒÆ’Ã‚Â¼lke, JÃƒÆ’Ã‚Â¶rg; Michna, Raphael; Commichau, Fabian; TÃƒÆ’Ã‚Â¶dter, Dominik; Zschiedrich, Christopher
Collaborative resource for the Bacillus community
database
summary
SubtiWiki
StÃƒÂ¼lke, JÃƒÂ¶rg; Zhu, Bingyao
No description supplied
database
summary
SugarBindDB
Lisacek, Frederique; Packer, Nicolle; Mariethoz, Julien; Campbell, Matthew Peter; Karlsson, Niclas; Alocci, Davide; Khatib, Khaled; Mullen, Elaine
Host-pathogen interactions mediated by glycans
database
summary
SulfAtlas
MICHEL, Gurvan; Stam, Mark; LeliÃ¨vre, Pernelle; Hoebeke, Mark; Corre, Erwan; Barbeyron, Tristan
Sulfatase families
database
summary
SUMMER
Wang, Meilin; Xin, Junyi; Chen, Silu; Ben, Shuai; Li, Huiqin; Zhang, Zhengdong; Du, Mulong
Biomarkers, GWAS and cancer survival
database
summary
SuperCAT
A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria
database
summary
SuperCYP
Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Guenther, Rainer Winnenburg, Michael Schroeder, and Robert Preissner
Cytochrome P450 alleles and drug interactions
database
summary
SuperDrug
Goede, A.
, Dunkel, M.
, Mester, N.
, Preissner, R.
A conformational drug database
database
summary
SuperDrug2
Preissner, Robert; Siramshetty, Vishal; Eckert, Andreas; Gohlke, BjÃƒÂ¶rn; Goede, Andrean; Chen, Qiaofeng; Devarakonda, Prashanth; Preissner, Saskia
No description supplied
database
summary
SUPERFAMILY
Oates, Matt; Stahlhacke, Jonathan; Vavoulis, Dimitrios; Smithers, Ben; Rackham, Owen; Sardar, Adam; Zaucha, Jan; Thurlby, Natalie; Fang, Hai; Gough, Julian
Assignments of proteins to structural superfamilies
database
summary
SuperFly
Jaeger, Johannes; Cicin-Sain, Damjan; Hermoso, Antonio; Crombach, Anton; Wotton, Karl; JimÃƒÂ©nez-Guri, Eva; Taly, Jean-FranÃƒÂ§ois; Roma, Guglielmo
spatio-temporal gene expression patterns indipteran embryos
database
summary
SuperHapten
Guenther S., Hempel D., Dunkel M., Rother K. and Preissner R.
A comprehensive database for small immunogenic compounds
database
summary
SuperNatural
Dunkel, Mathias; Banerjee, Priyanka; Erehman, Jevgeni; Gohlke, BjÃƒÂ¶rn; Wilhelm, Thomas; Preissner, Robert
Natural compounds and their suppliers
database
summary
SuperNatural
Gallo, Kathleen; Kemmler, Emanuel; Goede, Andrean; Becker, Finnja; Dunkel, Mathias; Preissner, Robert; Banerjee, Priyanka
SuperNatural 3.0 - a database of natural products
database
summary
SuperPain
Preissner, Saskia; Gohlke, BjÃƒÂ¶rn; Preissner, Robert
No description supplied
database
summary
SuperScent
Database of flavors and scents
database
summary
SuperSite
Dictionary of binding sites in proteins
database
summary
SuperSweet
Jessica Ahmed
, Saskia Preissner
, Mathias Dunkel
, Catherine L. Worth
,Andreas Eckert
and Robert Preissner
Natural and artificial sweetening agents
database
summary
SuperTarget
Hecker, Nikolai; Ahmed, Jessica; von Eichborn, Joachim; Dunkel, Mathias; Macha, Karel; Eckert, Andreas; Bourne, Phil; Gilson, Michael; Preissner, Robert
Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins
database
summary
SuperToxic
A comprehensive database of toxic compounds
database
summary
SUPFAM
Mudgal, R., Krishnadev, O., and Srinivasan, N.
This database elucidates the remote relationships found between Pfam families and structural families (SCOP) and uses the evolutionary information inherent of SCOP classification to identify related Pfam familiesRemote relationships between Pfam families.
database
summary
SureChEMBL
Hersey, Anne; Papadatos, George; Davies, Mark; Dedman, Nathan; Chambers, Jon; Gaulton, Anna; Siddle, James; Koks, Richard; Irvine, Sean; Pettersson, Joe; Goncharoff, Nicko; Overington, John
Chemical compounds extracted from patent documents
database
summary
SV4GD
Liang Cheng
Structural Variation for Genetic Diseases
database
summary
SVAtlas
Hou, Qingzhou; et al.
SVAtlas: A Comprehensive Single Extracellular Vesicle Omics Resource
database
summary
SWEET-DB
LoÃƒÅ¸, Alex
, Bunsmann. P.
, Bohne, A.
, LoÃƒÅ¸, Annika
, Schwarzer, E.
, Lang, E.
, von der Lieth, C.-W.
Annotated carbohydrate structure and substance information
database
summary
SWISS-2DPAGE
Hoogland C.
Annotated two-dimensional polyacrylamide gel electrophoresis database
database
summary
SWISS-MODEL Repository
Database of annotated 3D protein structure models
database
summary
SwissBioisostere
Zoete, Vincent; Cuozzo, Alessandro; Daina, Antoine; Perez, Marta; Michielin, Olivier
SwissBioisostere 2021: updated structural, bioactivity and physicochemical
database
summary
SwissBioisostere
Vincent Zoete
A database of molecular replacements for ligand design
database
summary
SwissRegulon
Pachkov M., Erb I., Molina N. and van Nimwegen E.
Genome-wide annotations of regulatory sites in the intergenic regions
database
summary
SwissSidechain
Vincent Zoete
No description supplied
database
summary
SYNBIP
Xue, Weiwei; WANG, Xiaona; Li, Fengcheng; QIU, Wenqi; XU, Binbin; LI, Yanlin; LIAN, Xichen; YU, Hongyan; ZHANG, Zhao; WANG, Jianxin; LI, Zhaorong; Zhu, Feng
Synthetic binding proteins
database
summary
SynDB
W. Zhang
, Y. Zhang
, H. Zheng
, C. Zhang
, W. Xiong
,J.G. Olyarchuk
, M. Walker
, W. Xu
, M. Zhao
, S. Zhao
, Z. Zhou
and L. Wei
Proteins involved in synaptic activity
database
summary
SynLethDB
Zheng, Jie; Guo, Jing; Liu, Hui
No description supplied
database
summary
SynSysNet
Robert Preissner
A database on the structural synaptome
database
summary
SyntDB:Ã‚Â defining orthologues of human long noncoding RNAs across primates
Bryzghalov, Oleksii;SzczeÃ…â€ºniak, MichaÃ…â€š Wojciech;MakaÃ…â€šowska, Izabela
No description supplied
database
summary
Synthetic Gene Database
Wu G., Zheng Y., Qureshi I., Zin H., Beck T., Bulka B. and Freeland S.J.
Synthetic genes described in peer-reviewed literature
database
summary
Sys-BodyFluid
Su-Jun Li, Mao Peng, Hong Li, Bo-Shu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li and Rong Zeng
Sys-BodyFluid is a body fluid proteome database for 11 fluids.
database
summary
SysPIMP
Platform for Identifying Mutated Proteins
database
summary
SysteMHC Atlas
Caron, Etienne; Shao, Wenguang; Pedrioli, Patrick; Wolski, Witold; Scurtescu, Cristian; Schmid, Emanuel; Vizcaino, Juan Antonio; Courcelles, Mathieu; Schuster, Heiko; Kowalewski, Daniel; Marino, Fabio; Arlehamn, Cecilia; Vaughan, Kerrie; Sette, Alessandro; Peters, Bjoern,; Ottenhoff, Tom; Meijgaarden, Krista; Nieuwenhuizen, Natalie; Kaufmann, Stefan; Schlapbach, Ralph; Castle, John; Nesvizhskii, Alexey; Nielsen, Morten; Deutsch, Erik; Campbell, David; Moritz, Robert; Zubarev, Roman; Ytterberg, Jimmy; Purcell, Anthony; Marcilla, Miguel; Paradela, Alberto; Wang, Qi; Costello, Catherine; Ternette, Nicola; van Veelen, Peter; Heck, Albert; van Els, CÃƒÂ©cile; de Souza, Gustavo A; Sollid, Ludvig; Admon, Arie; Stevanovic, Stefan; Rammensee, Hans-Georg; Thibault, Pierre; Perreault, Claude; Bassani-Sternberg, Michal; Aebersold, Ruedi
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire
database
summary
SysteMHC Atlas
Shao, Wenguang (proxy) (contact); Huang, Xiaoxiang; Gan, Ziao; Cui, Haowei; Lan, Tian; Liu, Yansheng; Caron, Etienne
The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
database
summary
SYSTERS
Krause, A.
, Haas, S.A.
, Coward, E.
, Vingron, M.
Integrated database of protein families, EST clusters and their genomic positions
database
summary
SYSTOMONAS
Choi C.
, MÜnch R.
, Leupold S.
, Klein J.
, Siegel I.
, Thielen B.
, Benkert B.
, Kucklick M.
, Schobert M.
, Barthelmes J.
, Ebeling C.
, Haddad I.
, Scheer M.
1,4
, Grote A.
, Hiller K.
, Boyke B.
, Schreiber K.
, Retter I.
, Schomburg D.
and Jahn D.
SYSTems biology of pseudOMONAS
database
summary
SZGR
Zhao, Zhongming; Jia, Peilin; Han, Guangchun; Zhao, Junfei; Lu, Pinyi
SchiZophrenia Gene Resource
database
summary
T-cell COVID-19 Atlas
Nersisyan, Stepan; Zhiyanov, Anton; Shkurnikov, Maxim; Tonevitsky, Alexander
Predicted affinities between SARS-CoV-2 peptides and HLA alleles
database
summary
T-psi-C: user friendly database of tRNA sequences and structures
Sajek, Marcin Piotr;WoÃ…Âºniak, Tomasz;Sprinzl, Mathias;Jaruzelska, Jadwiga;Barciszewski, Jan
tRNAs have been widely studied for their role as genetic code decoders in t
database
summary
T2D portal
This portal provides access to comprehensive results from 28 large human ge
database
summary
T3DB
Wishart, David; Arndt, David; Pon, Allison; Sajed, Tanvir; Guo, An Chi; Djoumbou, Yannick; Knox, Craig; Wilson, Michael ,; Liang, Jack; Grant, Jason; Liu, Yifeng; Goldansaz, Seyed; Rappaport, Stephen
Toxin and Toxin-Target Database
database
summary
Tabloid Proteome
Martens, Lennart; Gupta, Surya; Turan, Demet; Tavernier, Jan
No description supplied
database
summary
TADB
Yucheng Shao
, Ewan M. Harrison
, Dexi Bi1, Cui Tai
, Xinyi He
, Hong-Yu Ou
, Kumar Rajakumar
2,3
and Zixin Deng
Type II Toxin-Antitoxin loci in bacteria and archaea
database
summary
TADB
OU, Hong-Yu; Guan, Jiahao; Chen, Yongkui; Goh, Ying-Xian; Wang, Meng; Tai, Cui; Deng, Zixin1; Song, Jiangning
TADB 3.0: an updated database of bacterial toxin-antitoxin loci and associated mobile genetic elements
database
summary
TADB
Ou, Hong-Yu; Xie, Yingzhou; WEI, Yiqing; Shen, Yue; Li, Xiaobin; Zhou, Hao; Tai, Cui; Deng, Zixin
No description supplied
database
summary
TAED - The Adaptive Evolution Database
A phylogeny-based tool for comparative genomics
database
summary
TarBase
Vlachos, Ioannis; Paraskevopoulou, Maria; Karagkouni, Dimitra; Georgakilas, Georgios; Vergoulis, Thanasis; Kanellos, Ilias; Anastasopoulos, Ioannis-Laertes; Maniou, Sophia; Karathanou, Konstantina; Kalfakakou, Despina; Dalamagas, Thodoris; Hatzigeorgiou, Artemis
Database of experimental supported microRNA targets
database
summary
Tarbase
Hatzigeorgiou, Artemis; Skoufos, Giorgos; Kakoulidis, Panos; Tastsoglou, Spyros; Zacharopoulou, Elissavet; Kotsira, Vasiliki; Miliotis, Marios; Mavromati, Galatea; Grigoriadis, Dimitris; Zioga, Maria; Velli, Angeliki; Koutou, Ioanna; Karagkouni, Dimitra;
TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs
database
summary
Target-Pathogen
Fernandez Do Porto, Dario; Sosa, Ezequiel; Burguener, GermÃƒÂ¡n; Lanzarotti, Esteban; Defelipe, Lucas A; Radusky, Leandro; Pardo, AgustÃƒÂn; MartÃƒÂ, Marcelo; Turjanski, AdriÃƒÂ¡n
The successful use of antibiotics has been facing challenges because microb
database
summary
TargetDB
Target data from worldwide structural genomics projects
database
summary
TargetGene
Jia, Peilin; Lin, Shiqi; Wu, Song; Zhao, Wei27; Fang, Zhanjie; Hongen, Kang; Liu, Xinxuan; Pan, Siyu; Yu, Fudong; Bao, Yi-Ming
TargetGene: a comprehensive database of cell-type-specific target genes for genetic variants
database
summary
TassDB
Hiller M.
, Nikolajewa S.
, Huse K.
, Szafranski K.
, Rosenstiel P.
, Schuster S.
, Backofen R.
and Platzer M.
TAndem Splice Site DataBase
database
summary
tatDB
Grigoriev, Andrey; Guan, Lingyu
Experimentally supported targets of tRNA-derived fragments
database
summary
TBDB
Narasimhan, Kamesh; Marchand, Jorge; Smela, Merrick; Jordan, Thomas; Church, George
Structurally annotated T-box riboswitch: tRNA pairs
database
summary
TBDB
Stanford Tuberculosis Database
database
summary
TBestDB
O'Brien, E.A.
, Koski, L.
, Zhang, Y.
, Yang, L.
, Wang, E., Gray, M.W.
, Burger, G.
and Lang, B.F.
EST sequences and genes from unicellular eukaryotes
database
summary
TC3A
Li, Wei,; Feng, Xin; Li, Lei; Wagner, Eric
The Cancer 3' UTR Atlas
database
summary
TCDB
Saier Jr, Milton H.; Reddy, Vamsee S.; Moreno-Hagelsieb, Gabriel; Hendargo, Kevin J.; Zhang, Yichi; Iddamsetty, Vasu; Lam, Katie Jing Kay; Tian, Nuo; Russum, Steven; Wang, Jianing; Medrano-Soto, Arturo.
Transporter Classification Database
database
summary
TCGA SpliceSeq
Ryan, Michael; Wong, Wing Chung; Brown, Robert; Akbani, Rehan; Su, Xiaoping; Melott, James; Broom, Bradley; Weinstein, John
No description supplied
database
summary
TCMID
No description supplied
database
summary
TCMID
Tieliu Shi
Traditional Chinese Medicine Integrated Database
database
summary
TCOD
Zhao, Wen-Ming; Hailong, Kang; Huang, Tianhao; Duan, Guangya; Meng, Yuyan; Chen, Xiaoning; He, Shuang; Xia, Zhiqiang; Zhou, Xincheng; Chao, Jinquan; Tang, Bi-Xia; Wang, Zhonghuang; Zhu, Jun-Wei; Du, Zhenglin; sun, yanling; Zhang, Sisi; Xiao, Jingfa; Tian, Weimin; Wang, Wenquan
TCOD: an integrated resource for tropical crops
database
summary
TcoF-DB
Ulf Schaefer
, Sebastian Schmeier
and Vladimir B. Bajic
Database for Human Transcription Co-Factors
database
summary
TcoFBase
Li, Chunquan; Zhang, Yuexin; Song, Chao; Zhang, Yimeng; Wang, Yuezhu; Feng, Chenchen; Chen, Jia-Xin; Wei, Ling; Pan, Qi; Shang, Desi; Zhu, Yanbing; Zhu, Jiang',; Fang, Shuangsang; Zhao, Xilong; Xu, Xiaozheng; Wang, Qiuyu; Guo, Jin-Cheng
Transcription co-factors in human and mouse
database
summary
TCRD/Pharos
Edwards, Jeremy; Kelleher, Keith; Sheils, Timothy; Mathias, Stephen; Yang, Jeremy; Metzger, Vincent; Siramshetty, Vishal; Nguyen, Dac-Trung; Jensen, Lars,; Vidovic, Dusica; SchÃ¼rer, Stephan C.; Holmes, Jayme; Jones, Karlie; Pillai, Ajay; Bologa, Cristian;
Pharos integrates a new visualization from Reactome, which is available on all Target details pages. This tool helps you explore potential pathways for each target, based on pathways manually curated for interacting targets.
database
summary
TCRdb
Guo, Anyuan; Chen, Siyi; Yue, Tao; Lei, Qian
T-cell receptor (TCR) sequences
database
summary
TcruziDB
Trypanosoma cruzi
genome database
database
summary
TCSBN
Mardinoglu, Adil; Lee, Sunjae; Zhang, Cheng.'; Arif, Muhammad; Liu, Zhengtao; Benfeitas, Rui; Bidkhori, Gholamreza; Deshmukh, Sumit; Al Shobky, Mohamed; Lovric, Alen; Boren, Jan; Nielsen, Jens; UhlÃƒÂ©n, Matthias
No description supplied
database
summary
TcSNP
Genetic variation in Trypanosoma cruzi
database
summary
TDRtargets
Identification and ranking of targets against neglected tropical diseases
database
summary
TE-SCALE
ini Meng, Zhi Nie, Qifei Wang, Yiwen Hu, Yulan Deng, Na Ai, Zheng Huang, Yun Li, Yang Yuan, Jingfa Xiao, Jingyao Zeng, Guochao Li, Lan Jiang
TE-SCALE: a comprehensive database for exploring transposable elements and their regulatory functions in single cells
database
summary
TECRdb
Thermodynamics of enzyme-catalyzed reactions
database
summary
TED - Tomato Functional Genomics Database
Zhangjun Fei, Je-Gun Joung, Xuemei Tang, Yi Zheng, Mingyun Huang, Je Min Lee, Ryan McQuinn, Denise M. Tieman, Rob Alba, Harry J. Klee, and James J. Giovannoni
Tomato gene expression database
database
summary
TEDD
Cuidan Li; et al.
TEDD: A Comprehensive Resource for Translation Efficiency Dynamics
database
summary
TEDD
Dong, Zirui; Zhou, Ziheng; Tan, Cong; Chau, Matthew Hoi Kin; Jiang, Xiaosen; Ke, Ziyuan; Chen, Xiaoyan; Cao, Ye; Kwok, Yvonne K; Bellgard, Matthew; Leung, Tak Yeung; Choy, Kwong Wai
Temporal Expression of Development Database
database
summary
Telobase
FojtovÃ¡, Miloslava; LyÄ\x8Dka, Martin; BubenÃk, Michal; ZÃ¡vodnÃk, Michal; Peska, Vratislav; Fajkus, Petr; Demko, Martin; Fajkus, Jiri
TeloBase: a community-curated database of telomere sequences across the tree of life
database
summary
Telomerase database
Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components
database
summary
TESS
Transcription element search system
database
summary
TETSS
Zhang, Xiao-Ou; Gu, Xiaobing; Wang, Mingdong
TETSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS)
database
summary
TF-Marker
Li, Chunquan; Xu, Mingcong; Bai, Xuefeng; Ai, Bo; Zhang, Guorui; Song, Chao; Zhao, Jun; Wang, Yuezhu; Wei, Ling; Qian, Feng-Cui; Li, Yanyu; Zhou, Xinyuan; Zhou, Li-Wei; Yang, YongSan; Chen, Jia-Xin; Liu, Jiaqi; Shang, Desi; Wang, Xuan; Zhang, Jian'; Wang,
Human transcription factors, especially as cell markers
database
summary
TFBSbank
Chen, Dongsheng; Jiang, Sanjie; Ma, Xiaoyan; Li, Fang
Transcription factor binding profiles deduced from ChIP-seq or ChIP-chip data
database
summary
TFBSshape
Lin Yang
, Tianyin Zhou
, Iris Dror
, Anthony Mathelier
, Wyeth W. Wasserman
, Raluca GordÃƒÆ’Ã‚Â¢n
, and Remo Rohs
DNA shape features of transcription factor binding sites
database
summary
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites
Chiu, Tsu-Pei;Xin, Beibei;Markarian, Nicholas;Wang, Yingfei;Rohs, Remo
No description supplied
database
summary
TFcheckpoint
Acencio, Marcio; Vazquez, Miguel; Chawla, Konika; Lagreid, Astrid; Kuiper, Martin
TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat
database
summary
TFClass
Wingender, Edgar; Schoeps, Torsten; Haubrock, Martin; Doenitz, Juergen
TFClass: An expandable hierarchical classification of human transcription factors
database
summary
TFClass
Wingender, Edgar; Schoeps, Torsten; Haubrock, Martin; Krull, Mathias; Doenitz, Juergen
No description supplied
database
summary
TFSyntax
Zhao, Yongbing
Transcription Factor binding syntax
database
summary
TGD - Tetrahymena Genome Database
Stover, N.A., Krieger, C.J. and Cherry, J.M.
Tetrahymena thermophila genes, gene products and their annotations.
database
summary
The ABCD database: a repository for chemically defined antibodies
Lima, Wanessa C;Gasteiger, Elisabeth;Marcatili, Paolo;Duek, Paula;Bairoch, Amos;Cosson, Pierre
No description supplied
database
summary
The Autism Chromosome Rearrangement Database
Zhang J., Kanematsu E., Duggan G., Khaja R., MacDonald J.R. and Scherer S.W.
Curated collection of genomic features related to autism
database
summary
The Cell Cycle DB
Genes and proteins involved in human and yeast cell cycle
database
summary
The Chromosome 7 Annotation Project
MacDonald J.R., Cheung J., Zhang J., Khaja R., Duggan G., Kanematsu E. and Scherer S.W.
Human chromosome 7 sequence and annotation
database
summary
The European Bioinformatics Institute
Johanna McEntyre
Database resources of the European Bioinformatics Institute
database
summary
The Immune Epitope Database (IEDB): 2018 update
Vita, Randi;Mahajan, Swapnil;Overton, James A;Dhanda, Sandeep Kumar;Martini, Sheridan;Cantrell, Jason R;Wheeler, Daniel K;Sette, Alessandro;Peters, Bjoern
No description supplied
database
summary
The IUPHAR/BPS Guide to PHARMACOLOGY
Harding, Simon; Armstrong, Jane; Faccenda, Elena; Southan, Christopherinactive; Alexander, Stephen PH; Davenport, Anthony; Spedding, Michael; Davies, Jamie
The IUPHAR/BPS Guide to PHARMACOLOGY in 2024
database
summary
The Lafora Database
Zhang J., MacDonald J.R., Khaja R., Duggan G., Ianzano L., Chan E.M., Lohi H., Minassian B.A. and Scherer SW.
Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy
database
summary
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions
Newport, Thomas D;Sansom, Mark SÃ‚Â P;Stansfeld, Phillip J
No description supplied
database
summary
The Sequence Read Archive (SRA)
Yuichi Kodama, Martin Shumway and Rasko Leinonen
Sequence Read Archive
database
summary
The Signaling Pathways Project
Neil McKenna
Nuclear Receptor Signaling Atlas
database
summary
The Small Subunit rRNA Modification Database
Modified nucleosides in small subunit rRNA
database
summary
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
Nilsson, Rolf Henrik;Larsson, Karl-Henrik;Taylor, Andy FÃ‚Â S;Bengtsson-Palme, Johan;Jeppesen, Thomas S;Schigel, Dmitry;Kennedy, Peter;Picard, Kathryn;GlÃƒÂ¶ckner, Frank Oliver;Tedersoo, Leho;Saar, Irja;KÃƒÂµljalg, Urmas;Abarenkov, Kessy
No description supplied
database
summary
TheMarker
Chen, Yu Zong; ZHANG, Yintao; ZHOU, Ying; Zhou, Yuan; Yu, Xinyuan; Shen, Xinyi; Hong, Yanfeng; Zhang, Yuxin; Wang, Shanshan; Tao, Lin; Qiu, Yunqing; Zhu, Feng
TheMarker: a comprehensive database of therapeutic biomarkers
database
summary
ThermoMutDB
Pires, Douglas E.V.; Xavier, Joicymara; Rezende, PÃƒÂ¢mela; Velloso, JoÃƒÂ£o; Ascher, David
Protein Mutation Thermodynamics Database
database
summary
theRNA
Zhixiang Zuo; et al.
therna: a comprehensive database for RNA-based therapeutics
database
summary
THGS - Transmembrane Helices in Genome Sequences
Predicted transmembrane proteins
database
summary
Thing Metabolome Repository family
Sakurai, Nozomu; Yamazaki, Shinichi; Suda, Kunihiro; Hosoki, Ai; Akimoto, Nayumi; Takahashi, Haruya; Shibata, Daisuke; Aoki, Yuichi
LC-MS metabolomics data
database
summary
ThYme
David C. Cantu, Yingfei Chen, Matthew L. Lemons, and Peter J. Reilly
Thioester-active enzymes
database
summary
TIARA - Total Integrated Archive of short-Read and Array
Dongwan Hong
, Sung-Soo Park
, Young Seok Ju
1,3,4
, Sheehyun Kim
1,4
, Jong-Yeon Shin
1,2
, Sujung Kim
, Saet-Byeol Yu
, Won-Chul Lee
, Seungbok Lee
, Hansoo Park
, Jong-Il Kim
1,2,5
and Jeong-Sun Seo
1,2,3,4,5
Totally Integrated high-resolution Array cgh data and high-throughput sequencing Read data Archive for human whole genomes
database
summary
TIGR Maize database
Chan A.P.
, Pertea G.
, Cheung F.
, Lee D.
, Zheng L.
, Whitelaw C.
, Pontaroli A.C.
, SanMiguel P.
, Yuan Y.
, Bennetzen J.
, Barbazuk B.
, Quackenbush J.
1,6,7
and Rabinowicz P.D.
Maize genome sequencing consortium site
database
summary
TIGR Plant Transcript Assembly database
Childs K.L., Hamilton J., Zhu W., Ly E., Cheung F., Wu H., Rabinowicz P.D., Town C.D., Buell C.R., Chan A.P.
Transcript assemblies of plant EST and cDNA sequences
database
summary
TIGRFAMs
Functional identification of proteins
database
summary
TIMEDB
WANG, XUEYING; Chen, Lingxi; LIU, WEI; ZHANG, Yuanzheng; LIU, Dawei; ZHOU, Chenxin; SHI, Shuai; DONG, Jiajie; LAI, Zhentao; ZHANG, Wenjingyu; ZHAO, Bingran; CHENG, Haoyue; LI, Shuaicheng
RNAseq data and the tumor immune micro-environment
database
summary
TiProD
Chen X.
, Wu J.-M.
, Hornischer K.
, Kel A.
and Wingender E.
2,3
Human promoter sequences
database
summary
TISCH
Wang, Chenfei; Sun, Dongqing; Wang, Jin; Han, Ya; Dong, Xin; Zheng, Rongbin; Ge, Jun; Shi, Xiaoying; Wang, Binbin; Li, Ziyi,; Ren, Pengfei; Sun, Liangdong; Yan, Yilv; Zhang, Peng`; Zhang, Fan; Li, Taiwen
Uniformly processed tumor (and microenvironment) scRNA-seq data
database
summary
TISCH
Han, Ya; Wang, Yuting; Dong, Xin; Sun, Dongqing; Liu, Zhaoyang; Wang, Haiyun; Li, Taiwen; Wang, Chenfei
TISCH2: expanded datasets and new tools for single-cell transcriptome analy
database
summary
TISdb
Qian, Shu-Bing; Wan, Ji
A database of Translation Initiation Sites
database
summary
TISMO
Zeng, Zexian; Wong, Cheryl; Yang, Lin; Ouardaoui, Nofal; Li, Dian; Zhang, Wubing; Gu, Shengqing; Zhang, Yi; Liu, Yang; Wang, Xiaoqing; Fu, Jingxin; Zhou, Liye; Zhang, Boning; Kim, Sarah; Yates, Kathleen B; Brown, Myles; Freeman, Gordon J.; Uppaluri, Ravin
Mouse syngeneic tumor models
database
summary
TissGDB
Zhao, Zhongming; Kim, Pora; Park, Aekyung; Han, Guangchun; Sun, Hua; Jia, Peilin
Tissue-specific gene expression is critical in understanding biological pro
database
summary
TissueNet
Esti Yeger-Lotem
Tissue distribution of protein-protein interactions
database
summary
TissueNexus
Wang, Jianxin; Lin, Cuixiang; Li, Hongdong,; Deng, Chao; Guan, Yuanfang
Tissue or cell line functional gene networks
database
summary
TmAlphaFold
TusnÃ¡dy, GÃ¡bor; Dobson, LÃ¡szlÃ³; Szekeres, Levente; GerdÃ¡n, Csongor; LangÃ³, TamÃ¡s; Zeke, AndrÃ¡s
AlphaFold TM protein predictions, membrane-embedded and assessed
database
summary
tModBase
Lei, Hao-Tian; Wang, Zhang-Hao; Li, Bin ,; Sun, Yang; Mei, Shi-Qiang; Yang, Jian-Hua; Qu, Liang-Hu; Zheng, Lingling
tRNA modifications: enzymes, dynamics, diseases
database
summary
TMPad
Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung, and Wen-Lian Hsu
Helix-packing folds in transmembrane proteins
database
summary
tmRDB
Burks, J
, Zwieb, C
, Gorodkin, J
, Knudsen, B
and Wower, J
tmRNA (10Sa RNA) sequences and alignments
database
summary
TomatEST DB
D'Agostino N.
, Aversano M.
, Frusciante L.
and Chiusano M.L.
EST collection from multiple tomato species
database
summary
TopDB
TusnÃƒÂ¡dy, GÃƒÂ¡bor; Dobson, LÃƒÂ¡szlÃƒÂ³; LangÃƒÂ³, TamÃƒÂ¡s; RemÃƒÂ©nyi, IstvÃƒÂ¡n
Topology Data Bank of transmembrane proteins
database
summary
TopFIND
Nikolaus Fortelny
1,2,3,4
, Sharon Yang
3,5,6
, Paul Pavlidis
4,7
, Philipp F. Lange
2,3,*
and Christopher M. Overall
1,2,3,*
Protein N- and C-termini and protease processing
database
summary
TopoSNP
Topographic database of non-synonymous SNPs
database
summary
TOPPR
Lennart Martens
The Online Protein Processing Resource
database
summary
TOPSAN
Kyle Ellrott
1,2
, Christian M. Zmasek
3,4
, Dana Weekes
1,4,
S. Sri Krishna
,4
Constantina Bakolitsa
1,4
, Adam Godzik
1,2,3,4
and John Wooley
1,2,4
The Open Protein Structure Annotation Network
database
summary
ToxoDB - The
Toxoplasma gondii
Genome Database
Kissinger, J.C.
, Gajria, B.
, Li, L.
, Paulsen, I.T.
, Roos, D.S.
Apicomplexan parasite Toxoplasma gondii genome
database
summary
TOXRIC
Bo, Xiaochen; Wu, Lianlian; Yan, Bowei; Han, Junshan; He, Song
Toxicological data and benchmarks
database
summary
TPDDb
Zhou, Ying; et al.
TPDDb: the comprehensive database of targeted protein degrader (TPD)
database
summary
TPIA
Xia, Enhua; Gao, Qijuan; Tong, Wei; Li, Fangdong; Wang, Yanli; Wu, Qiong; Wan, Xiaochun
TPIA2: an updated tea plant information archive for Camellia genomics
database
summary
TPMD - Taiwan polymorphic microsatellite marker database
Microsatellite markers genotyped in Taiwanese populations
database
summary
TRACTOR db
abelito@bioinfo.cu
Transcription factors in gamma-proteobacteria database
database
summary
TransCirc
Wang, Zefeng; Huang, Wendi; Ling, Yunchao; Zhang, Sirui; Xia, Qiguang; Cao, Rui-Fang; Fan, Xiao-Juan; Zhang, Guo-Qing
Protein coding potential of circRNAs
database
summary
TRANSCompel
Kel-Margoulis, O.
, Kel, A.
, Reuter, I.
, Deineko, I.
, Wingender, E.
Transcriptional regulation, composite regulatory elements
database
summary
TranscriptDB
Aida Ouangraoua
Eukaryotic transcript conservation and evolution
database
summary
TRANSFAC
Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., and Wingender, E.
Transcription factors, gene regulation, positional weight matrices
database
summary
Transformer
Preissner, Saskia; Hoffmann, Michael; Preissner, Sarah; nickel, janette; Dunkel, Mathias; Preissner, Robert
Biotransformation of xenobioitics - drugs and food ingredients - by human enzymes
database
summary
TranslatomeDB
Zhang, Gong '; Liu, Wanting; Xiang, Lunping; Zheng, Tingkai
No description supplied
database
summary
TransLnc
Li, Yongsheng; Lv, Dezhong; Chang, Zhenghong; Cai, Yangyang; Li, Junyi; Wang, Liping; Jiang, Qiushuang; Xu, Kang1; Ding, Na; Li, Xia; Xu, Juan,
Coding potential of lncRNAs across tissues, including neoantigens
database
summary
TransmiR
Juan Wang, Ming Lu, Chengxiang Qiu, and Qinghua Cui
Regulatory relations between transcription factors and microRNAs
database
summary
TransmiR v2.0: an updated transcription factor-microRNA regulation database
Tong, Zhan;Cui, Qinghua;Wang, Juan;Zhou, Yuan
No description supplied
database
summary
TRANSPATH
Krull, M.
, Pistor, S.
, Voss, N.
, Kel, A.
, Reuter, I.
, Potapov, A.
1,2
, Choi, C.
, Kel-Margoulis, O.
, Wingender, E.
1,2
Signal transduction pathways, vizualization and expression data analysis
database
summary
TranspoGene
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates
database
summary
TransportDB
Sequences and classification of predicted membrane transporters encoded in complete genomes
database
summary
TRBase
Boby T., Patch A.-M. and Aves S.J.
Tandem repeats in the human genome
database
summary
TRDB
Tandem repeats in genomic DNA
database
summary
TRED - Transcriptional Regulatory Element Database
Transcriptional regulatory element database
database
summary
Tree of Life
Information on phylogeny and biodiversity
database
summary
TreeBase
Piel W.H.
and Miller M.A.
Phylogenetic trees and the data matrices used to generate them
database
summary
TreeFam
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Tree families database: phylogenetic trees of animal genes
database
summary
tRFdb
Dutta, Anindya; kumar, pankaj; Mudunuri, Suresh; Anaya, Jordan
Short (14-32 nt) tRNA-related fragments
database
summary
tRFtarget
Wang, Zuoheng; Li, Ningshan; Shan, Nayang; Lu, Lingeng
Targets of tRNA-derived fragments
database
summary
tRFtarget
Wang, Zuoheng; Li, Ningshan; Yao, Siqiong; Yu, Guangjun; Lu, Lingeng
tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments
database
summary
TriForC database
Goossens, Alain; Miettinen, Karel; IÃƒÂ±igo, Sabrina; Kreft, Lukasz; Pollier, Jacob; De Bo, Christof; Botzki, Alexander; Coppens, Frederik; Bak, SÃƒÂ¸ren
No description supplied
database
summary
TRIP
Young-Cheul Shin
, Soo-Yong Shin
, Insuk So
, Dongseop Kwon
, and Ju-Hong Jeon
Protein-protein interactions for mammalian TRP channels
database
summary
TriTrypDB
Functional genomic data for Trypanosomatid pathogens
database
summary
tRNAdb
Joern Puetz
Compilation of tRNA sequences and tRNA genes
database
summary
tRNADB-CE
tRNA Gene DataBase Curated by Experts
database
summary
trome, trEST and trGEN
Databases of predicted human protein sequences
database
summary
TropGENE DB
Ruiz, M.
Genetics and genomics of tropical crops: sugarcane, banana, cocoa
database
summary
TRRUST v2
Lee, Insuk; Han, Heonjong; Cho, Jae-Won; Lee, Sangyoung; Yun, Ayoung; Kim, Hyojin; Bae, Dasom; Yang, Sunmo; Kim, Chanyoung; Lee, Muyoung; Kim, Eunbeen; Lee, Sungho; Kang, Byunghee; Jeong, Dabin; Kim, Yaeji; Jeon, Hyeon-Nae; Jung, Haein; Nam, Sunhwee; Chung, Michael; Kim, Jong-Hoon
No description supplied
database
summary
TrSDB
Antoni Hermoso, Daniel Aguilar, Francesc X. Aviles, Enrique Querol
TrSDB is a Biological Proteome KnowledgeBase linking IPI and SPTR-NR based
database
summary
TrypanoCyc
Jourdan, Fabien; Shameer, Sanu; Logan-Klumper, Flora; Vinson, Florence; COTTRET, Ludovic; Merlet, Benjamin; Achcar, Fiona; Boshart, Michael; Berriman, Matt; Breitling, Rainer; Bringaud, FrÃƒÂ©dÃƒÂ©ric; BÃƒÂ¼tikofer, Peter; Cattanach, Amy; Bannerman-Chukualim, Bridget; Creek, Darren; Crouch, Kathryn; de Koning, Harry; Denise, Hubert; Ebikeme, Charles; Fairlamb, Alan; Ferguson, Michael; Hertz-Fowler, Christiane; Kerkhoven, Eduard; MÃƒÂ¤ser, Pascal; Michels, Paul; Nayak, Archana; Nolan, Derek; Olsen, Christian; Silva-Franco, Fatima; Smith, Terry; Taylor, Martin; Tielens, Aloysius; Urbaniak, Michael; van Hellemond, Jaap; Vincent, Isabel; Wilkinson, Shane; Wyllie, Susan; Opperdoes, Fred; Barrett, Mike; Ginger, Michael
Biochemical pathways of Trypanosoma brucei
database
summary
TSGene
Zhongming Zhao
Tumor Suppressor Gene database
database
summary
tsRBase
Peng, Yong; Zuo, Yuanli; Zhu, Lei; Guo, Zhixin; Liu, Wenrong; Zhang, Jiting; Zeng, Zhen; Wu, Qingbin; Cheng, Jian; Fu, Xin; Jin, Yang; Zhao, Yun
tRNA-derived small RNA expression and function
database
summary
tsRFun
Zheng, Lingling; Wang, Junhao; Chen, Wenxin; Yang, Yuedong.; Yang, Jian-Hua; Qu, Liang-Hu
tsRNA expression and networks
database
summary
TSTMP
Julia Varga
1,2
, LÃƒÂ¡szlÃƒÂ³ Dobson
, IstvÃƒÂ¡n RemÃƒÂ©nyi
and GÃƒÂ¡bor E. TusnÃƒÂ¡dy
Target Selection database for human TransMembrane Proteins
database
summary
TTD
Chen, Yu Z; et al.
Therapeutic target database 2026: facilitating the targeted therapies and precision medicine by providing multi-omics clinical and target information
database
summary
TTD
Chen, Yu Zong; Zhang, Yintao; Zhou, Ying; Xu, Hangwei; Jiang, Wanghao; Li, Bo; Lai, Dianyu; Wan, Cong; Wang, Shanshan; Zhao, Mingxiao; Tan, Ying'; Lu, Songlin; Fan, Tingting; Liu, Xin; Zhu, Feng
Therapeutic Target Database
database
summary
TTD
Chen, Yu Zong; ZHOU, Ying; ZHANG, Yintao; LIAN, Xichen; Li, Fengcheng; Wang, Chaoxin; Zhu, Feng; Qiu, Yunqing
Therapeutic target database update 2022: facilitating drug discovery with e
database
summary
TTD
Chen, Yu Zong; ZHOU, Ying; ZHANG, Yintao; Zhao, Donghai; Yu, Xinyuan; Shen, Xinyi; Zhou, Yuan; Wang, Shanshan; Qiu, Yunqing; Zhu, Feng
Therapeutic Target Database Update 2024: Enriched Information for Target Druggability from Multiple Perspectives
database
summary
TTD
Chen, Yu-Zong; Li, Ying Hong; Yu, Chun Yan; Li, Xiao Xu; Zhang, Peng; Tang, Jing; Yang, Qingxia; Fu, Tingting; Zhang, Xiaoyu; Cui, Xuejiao; Tu, Gao; Zhang, Yang; Li, Shuang,; Yang, Fengyuan; Sun, Qiu; Qin, Chu; Chen, Zhe; Zhu, Feng
No description supplied
database
summary
TTD - Therapeutic Target Database
Chen, Yu Zong; Qin, Chu; Zhang, Cheng; Feng, Xu; Zhu, Feng; Chen, Shang Ying; Zhang, Peng;
Therapeutic Target Database
database
summary
TTDB
Zhi Xie; et al.
TTDB: a comprehensive transcriptome turnover database for exploring mRNA stability
database
summary
TTSMI (temporarily unavailable)
Jenjaroenpun, Piroon; Chew, Chee; YONG, Taipang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir
Triplex Target DNA Sites in the human genome
database
summary
Tumor Associated Gene database
Chan H.-H.
, Tsai S.-J.
2,3
, Sun H.S.
1,3
Tumor-associated genes
database
summary
TumorFusions
Zheng, Siyuan; Hu, Xin; Wang, Qianghu; Tang, Ming; Barthel, Floris; Amin, Samirkumar; Yoshihara, Kosuke; Lang, Frederick; Martinez-Ledesma, Emmanuel; Lee, Soo Hyun; Verhaak, Roel
No description supplied
database
summary
TWAS Atlas
Xiao, Jingfa; Lu, Mingming; Zhang, Yadong; Yang, Fengchun; Mai, Jialin; Gao, Qainwen; Xu, Xiaowei; Kang, Hongyu; Hou, Li; Shang, Yunfei; Qian, Qiheng; Liu, Jie; Jiang, Meiye; Zhang, Hao; Bu, Congfan; Wang, Jinyue; Zhang, Zhewen; Zhang, Zaichao; Zeng, Jing
Transcriptome-wide association studies
database
summary
U12DB
Alioto T.
A database of orthologous U12-type spliceosomal introns
database
summary
Ubibrowser
Li, Dong; Wang, Xun; Li, Yang; He, Mengqi; Kong, Xiangren; Jiang, Peng; Liu, Xi; Diao, Lihong; Zhang, Xinlei; Li, Honglei; Ling, Xinping; Xia, Simin; Liu, Zhongyang; Liu, Yuan; Cui, Chun-Ping; Wang, Yan; Tang, Liujun; Zhang, Lingqiang; He, Fuchu
Proteome-wide ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotes
database
summary
UCbase and miRfunc
Database of Ultraconserved sequences and microRNA function
database
summary
UCNEbase
Philipp Bucher
A database of ultraconserved non-coding elements and gene regulatory blocks
database
summary
UCSC Archaeal Genome Browser
Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran and Todd M. Lowe
The UCSC Archaeal Genome Browser
database
summary
UCSC Cancer Genomics Browser
Goldman, Mary; Craft, Brian; Swatloski, Teresa; Cline, Melissa; Morozova, Olena; Diekhans, Mark; Haussler, David; Zhu, Jingchun
Web-based tools to integrate, visualize and analyze cancer genomics and clinical data
database
summary
UCSC Genome Browser
Brian Raney
Genome assemblies and annotation
database
summary
UCSC Genome Browser
Jonathan Casper; et al.
The UCSC Genome Browser database: 2026 update
database
summary
UCSC Genome Browser
Tyner, Cath
, Barber, Galt P.
, Casper, Jonathan
, Clawson, Hiram
, Diekhans, Mark
, Eisenhart, Christopher
, Fischer, Clayton M.
, Gibson, David
, Navarro Gonzalez, Jairo
, Guruvadoo, Luvina
, Haeussler, Maximilian
, Heitner, Steve
, Hinrichs, Angie S.
, Karolchik, Donna
, Lee, Brian T.
, Lee, Christopher M.
, Nejad, Parisa
, Raney, Brian J.
, Rosenbloom, Kate R.
, Speir, Matthew L.
, Villarreal, Chris
, Vivian, John
, Zweig, Ann S.
, Haussler, David
1,3
, Kuhn, Robert M.
, and Kent, W. James
Genome assemblies and annotation
database
summary
UCSC Genome Browser
Raney, Brian; Barber, Galt; Benet PagÃ¨s, Anna; Casper, Jonathan; Clawson, Hiram; Cline, Melissa; Diekhans, Mark; Fischer, Clayton; Navarro Gonzalez, Jairo; Hickey, Glenn; Hinrichs, Angie; Kuhn, Robert; Lee, Brian; Lee, Christopher; Le Mercier, philippe; Miga, Karen H.; Nassar, Luis; Nejad, Parisa; Paten, Benedict; Perez, Gerardo; Schmelter, Daniel; Speir, Matthew; Wick, Brittney; Zweig, Ann; Haussler, David; Kent, James; Haeussler, Maximilian
The UCSC Genome Browser database provides high-quality genomics data visual
database
summary
UCSD-Nature Signaling Gateway Molecule Pages
Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling
database
summary
UET
Lua, Rhonald; Wilson, Stephen; Konecki, Daniel; Wilkins, Angela; Venner, Eric; Morgan, Daniel; Lichtarge, Olivier
Universal Evolutionary Trace database
database
summary
UFCG
Kim, Dongwook; Gilchrist, Cameron; Chun, Jongsik; Steinegger, Martin
Fungal core genes
database
summary
UgMicroSatdb
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes
database
summary
UMD-BRCA1/BRCA2 databases
Sandrine Caputo
BRCA1 and BRCA2 mutations detected in France
database
summary
UniCarbKB
Packer, Nicolle; Campbell, Matthew; Peterson, Robyn; Mariethoz, Julien; Gasteiger, Elisabeth;
N- and O-linked glycan structures and biological sources
database
summary
Uniclust
Steinegger, Martin; Mirdita, Milot; von den Driesch, Lars; Galiez, Clovis; Martin, Maria; SÃƒÂ¶ding, Johannes
Clustered protein sequences and multiple sequence alignments
database
summary
UniHI
Futschik, Matthias; Kalathur, Ravi; Pinto, JosÃƒÆ’Ã‚Â©; Hernandez-Prieto, Miguel; Machado, Rui; Chaurasia, Gautam
Unified Human Interactome: human protein-protein interactions
database
summary
UniLectin
Lisacek, Frederique; Schnider, Boris; M'Rad, Yacine; El Ahmadie, Jalaa; de Brevern, Alexandre; Imberty, Anne
HumanLectome, an update of UniLectin for the annotation and prediction of human lectins
database
summary
UniParc
Apweiler R.
, Bairoch A.
and Wu C.H.
3,4
UniProt archive: a repository of all protein sequences
database
summary
UniPathway
Anne Morgat
Metabolic pathway information in UniProt knowledge base
database
summary
UniPROBE
Hume, Maxwell; Barrera, Luis; Gisselbrecht, Steve; Bulyk, Martha
Universal Protein binding microarray Resource for Oligonucleotide Binding Evaluation
database
summary
UniProt
Alex Bateman
All known protein sequences
database
summary
UniProt
Orchard, Sandra
UniProt: The Universal Protein Knowledgebase in 2023
database
summary
UniRef
Apweiler R.
, Bairoch A.
and Wu C.H.
3,4
UniProt non-redundant reference databases: clustered sets of related sequences.
database
summary
UniSave
Apweiler R.
, Bairoch A.
and Wu C.H.
3,4
UniProtKB Sequence/Annotation Version Archive
database
summary
UniSTS
Unified non-redundant view of sequence tagged sites with marker and mapping data from a variety of resources
database
summary
UNITE
Abarenkov, Kessy; Nilsson, Henrik; Larsson, Karl-Henrik; Taylor, Andy F. S.; May, Tom; FrÃ¸slev, Tobias; Pawlowska, Julia; Lindahl, BjÃ¶rn; PÃµldmaa, Kadri; Truong, Camille; Vu, Duong; Hosoya, Tsuyoshi; Niskanen, Tuula; Piirmann, Timo; Ivanov, Filipp; Zirk, Allan; Peterson, Marko; Cheeke, Tanya; Ishigami, Yui; Jansson, Arnold; Jeppesen, Thomas; Kristiansson, Erik,; Mikryukov, Vladimir; Miller, Joseph; Oono, Ryoko; Ossandon, Francisco; PaupÃ©rio, Joana; Saar, Irja; Schigel, Dmitry; Suija, Ave; Tedersoo, Leho; Koljalg, Urmas
The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa, and classifications reconsidered
database
summary
UniTmp
TusnÃ¡dy, GÃ¡bor; Dobson, LÃ¡szlÃ³; GerdÃ¡n, Csongor; TusnÃ¡dy, Simon; Szekeres, Levente; Kuffa, Katalin; LangÃ³, TamÃ¡s; Zeke, AndrÃ¡s
UniTmp: Unified resources for transmembrane proteins
database
summary
UniTrap
Unambiguous insertions in the same subgenic regions of annotated mouse genes
database
summary
UniVec
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
database
summary
University of Pittsburgh Bioinformatics Resources Collection
Chen Y.-B.
, Chattopadhyay A
, Bergen P.
, Gadd C.
, Tannery, N.
A collection of bioinformatic databases and software tools
database
summary
uORFdb
Manske, Felix; Ogoniak, Lynn; JÃ¼rgens, Lara; Grundmann, Norbert; MakaÅ‚owski, Wojciech; Wethmar, Klaus
The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research
database
summary
uORFdb
Wethmar, Klaus; Barbosa da Silva, Adriano; Andrade-Navarro, Miguel; Leutz, Achim
Upstream ORFs and their effect of translation of downstream CDSs
database
summary
UTexas Aptamer Database
Stovall, Gwendolyn; Askari, Ali; Kota, Sumedha; Ferrell, Hailey; Swamy, Shriya; Goodman, Kayla; Okoro, Christine; Spruell Crenshaw, Isaiah; Hernandez, Daniela; Oliphant, Taylor; Badrayani, Akshata; Ellington, Andrew
UTexas Aptamer Database: The Collection and Long-Term Preservation of Aptamer Sequence Information
database
summary
UTGB/medaka
University of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data
database
summary
UTRdb
Lo Giudice, Claudio; Zambelli, Federico.; Chiara, Matteo; Pavesi, Giulio; Tangaro, Marco Antonio; Picardi, Ernesto; Pesole, Graziano
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untr
database
summary
UTRdb/UTRsite
Pesole, G.
, Liuni, S.
, Grillo, G.
, Licciulli, F.
, Mignone, F.
, Gissi, C.
, Saccone, C.
5' and 3' UTRs of eukaryotic mRNAs and relevant functional patterns
database
summary
UTRome
3'UTRs and their functional elements in C. elegans
database
summary
VADE
Imanishi, Tadashi; Nagai, Yoko; Takahashi, Yasuko
VarySysDB Disease Edition: Disease-associated genomic polymorphisms
database
summary
ValidatorDB
Sehnal, David; SvobodovÃƒÂ¡ VaÃ…â„¢ekovÃƒÂ¡, Radka; Pravda, LukÃƒÂ¡Ã…Â¡; Ionescu, Crina-Maria; Geidl, Stanislav; HorskÃƒÂ½, VladimÃƒÂr; Jaiswal, Deepti; Wimmerova, Michaela; KoÃ„\x8Da, Jaroslav
Precomputed validation results for ligands and residues in the PDB
database
summary
ValidNESs
Hsueh-Fen Juan
No description supplied
database
summary
VannoPortal
Li, Mulin Jun; Huang, Dandan; Zhou, Yao1; Yi, Xianfu; Fan, Xutong; Wang, Jianhua; Yao, Hongcheng; Sham, Pak
Human genetic variants vs traits and diseases
database
summary
VARAdb
Li, Chunquan; Pan, Qi; Liu, Yuejuan; Bai, Xuefeng; Han, Xiaole; Jiang, Yong'; Ai, Bo; Shi, Shanshan; Wang, Fan,; Xu, Mingcong; Wang, Yuezhu; Zhao, Jun; Chen, Jia-Xin; Zhang, Jian'; Li, Xuecang; Zhu, Jiang',; Zhang, Guorui; Wang, Qiuyu
Variants and regulatory information
database
summary
VarCards
Sun, zhongsheng; Li, Jinchen; Shi, Leisheng; Zhang, Kun; Zhang, Yi; Zhao, Tingting; Teng, Huajing; Li, Xianfeng'; Jiang, Yi; Ji, Liying
No description supplied
database
summary
VarCards
Li, Jinchen; Wang, Zheng; Zhao, Guihu; Zhu, Zhaopo; Zhang, Shiyu; Wang, Yijing; Luo, Tengfei; Zhou, Qiao; Qiu, Jian; Tang, Beisha; Xia, Kun; Li, Bin
VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in human whole genome
database
summary
VarEPS
Wu, Linhuan; Sun, Qinglan; Shu, Chang; Shi, Wenyu; Luo, Yingfeng; Fan, Guomei; Nie, Jingyi; Bi, Yuhai; Wang, Qihui; Qi, Jianxun; Lu, Jian; Zhou, Yuanchun; Shen, Zhihong; Meng, Zhen; Zhang, Xinjiao; Yu, Zhengfei; Gao, Shenghan; Ma, Juncai; Hu, Songnian
SARS-CoV-2 variants, known and theoretical, vs therapies
database
summary
VarEPS-influ
Wu, Linhuan; Shu, Chang; Sun, Qinglan; Fan, Guomei; Peng, Kesheng; Yu, Zhengfei; Luo, Yingfeng; Gao, Shenghan; Deng, Tao; Ma, Juncai; Hu, Songnian
VarEPS-Influï¼šan evaluation and prewarning system of occurred and virtual variations of Influenza Virus genomes
database
summary
VARIDT
Fu, Tingting; et al.
VARIDT 2026: The updated database of genetic variants that impact drug therapy
database
summary
VARIDT
Zhu, Feng; Fu, Tingting; Li, Fengcheng; Zhang, Yang; Yin, Jiayi; QIU, Wenqi; Li, Xuedong; Liu, Xingang; Xin, Wenwen; Wang, Chengzhao; Yu, Lushan; Zheng, Qingchuan; Zeng, Su
VARIDT 2.0: Structural Variability of Drug Transporter
database
summary
VARIDT
Jiayi Yin, Wen Sun, Fengcheng Li, Jiajun Hong, Xiaoxu Li, Ying Zhou, Yinjing Lu, Mengzhi Liu, Xue Zhang, Na Chen, Xiuping Jin, Jia Xue, Su Zeng, Lushan Yu, Feng Zhu
Database of genetic variants that impact drug therapy
database
summary
VARIDT
Zhu, Feng; Yin, Jiayi; CHEN, Zhen; You, Nanxin; Li, Fengcheng; Zeng, Su
VARIDT 3.0: regulatory variability of drug transporter
database
summary
VarySysDB
Various types of human gene polymorphism
database
summary
VBASE2
Retter, I.
, Althaus, H.H.
2,3
, MÜnch, R.
and MÜller, W.
Variable genes from the Ig loci of human and mouse
database
summary
VDGE
Yong Zhang
Variation Database of Gene-Edited animals
database
summary
VDJdb
Chudakov, Dmitry; Shugay, Mikhail; Bagaev, Dmitriy; Zvyagin, Ivan; Vroomans, Renske; Crawford, Jeremy; Dolton, Garry; Komech, Ekaterina; Sycheva, Anastasiya; Koneva, Anna; van Dyk, Ewald; Dash, Pradyot; Attaf, Meriem; Rius, Cristina; Ladell, Kristin; McLaren, James; Clemens, E; Douek, Danny; Luciani, Fabio; van Baarle, D; Kesmir, Can; Kedzierska, Katherine; Thomas, Paul G; Price, David A; Sewell, Andy
The primary goal of VDJdb is to facilitate access to existing information o
database
summary
VectorBase
Emrich, Scott; Giraldo-Calderon, Gloria; MacCallum, Robert; Maslen, Gareth; Gesing, Sandra; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Madey, Greg; Collins, Frank; Lawson, Dan
Invertebrate Vectors of Human Pathogens
database
summary
VectorDB
Characterization and classification of nucleic acid vectors
database
summary
VEGA
Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG.
Vertebrate genome annotation database (discontinued)
database
summary
Vesiclepedia
Mathivanan, Suresh; Chitti, Sai V.; Gummadi, Sriram; Kang, Taeyoung; Shahi, Sanjay; Marzan, Akbar L.; Nedeva, Christina; Sanwlani, Rahul; Bramich, Kyle; Stewart, Sarah; Petrovska, Monika; Sen, Biswadeep; Ozkan, Alper; Akinfenwa, Maria; Fonseka, Pamali
Vesiclepedia 2024: An extracellular vesicles and extracellular vesicle-like nanoparticles repository
database
summary
VEuPathDB
Harb, Omar; Amos, Beatrice; Aurrecoechea, Cristina; Barba, Matthieu; Barreto, Anna; Basenko, Evelina; BaÅ¼ant, Wojciech; Belnap, Robert; Blevins, Ann; Boehme, Ulrike; Brestelli, John; Brunk, Brian; Caddick, Mark; Callan, Danielle; Christensen, Mikkel; Chri
Genomics of eukaryote pathogens and their vectors [CHECK]
database
summary
VEuPathDB
Warrenfeltz, Susanne; Alvarez-Jarreta, Jorge; Amos, Beatrice; Aurrecoechea, Cristina; Bah, Saikou; Barba, Matthieu; Barreto, Anna; Basenko, Evelina; Belnap, Robert; Blevins, Ann; Boehme, Ulrike; Brestelli, John; Brown, Stuart; Callan, Danielle; Campbell, Lahcen; Christophides, George; Crouch, Kathryn; Davison, Helen; DeBarry, Jeremy; Demko, Richard; Douherty, Ryan; Duan, Yikun; Dundore, Walter; Dyer, Sarah; Falke, Dave; Fisher, Steve; Gajria, Bindu; Galdi, Daniel; Giraldo-Calderon, Gloria; Harb, Omar; Harper, Elizabeth; Helb, Danica; Howington, Connor; Hu, Sufen; Humphrey, Jay; Iodice, John; Jones, Andrew; Judkins, John; Kelly, Sarah; Kissinger, Jessica; Kittur, Nupur; Kwon, Dae; Lamoureuxx, Kristopher; Li, Wei; Lodha, Disha; MacCallum, Robert; Maslen, Gareth; McDowell, Mary Ann; Myers, Jeremy; Mural, Mustafa; Roos, David; Rund, Samuel; Shanmugasundram, Achchuthan; Sitnik, Vasily; Spruill, Drew; Starns, David; Tomko, Sheena; Wang, Haiming; Wieck, Robert; Wilkinson, Paul; Zheng, Jie2
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.
database
summary
VFDB
Yang, Jian; Liu, Bo `; Zheng, Dandan; Zhou, Siyu,; Chen, Lihong,
VFDB a general classification scheme for bacterial virulence factors
database
summary
VFDB - Virulence Factors Database
Liu, Bo; Zheng, Dandan; Zhou, Siyu; Chen, Lihong; Yang, Jian
Reference database for microbial virulence factors
database
summary
ViBrism DB
Masahiko Morita
, Kazuro Shimokawa
, Masaomi Nishimura
, Sakiko Nakamura
, Yuki Tsujimura
, Satoko Takemoto
, Takehiro Tawara
, Hideo Yokota
, Shuhei Wemler
, Daisuke Miyamoto
, Hidetoshi Ikeno
, Akira Sato
, Teiichi Furuichi
, Norio Kobayashi
, Yoshihiro Okumura
, Yoko Yamaguchi
and Yuko Okamura-Oho
1,9
ViBrism DB (http://vibrism.neuroinf.jp/) is a database for anatomical gene
database
summary
VIDA
Virus genome open reading frames
database
summary
ViMIC
Zhang, Xiaoyan; Wang, Ying; Tong, Yuantao; Zhang, Zeyu; Zheng, Rongbin; Huang, Danqi; Yang, Jinxuan; Zong, Hui; Tan, Fanglin; Xie, Yujia; Huang, Honglian
Virus Mutations, Integration sites and Cis-effects
database
summary
VIOLIN
He, Yongqun; Racz, Rebecca; Sayers, Samantha; Lin, Yu; Todd, Thomas; Hur, Junguk; Li, Xinna; Patel, Mukti; Zhao, Boyang; Chung, Monica; Ostrow, Joseph; Sylora, Andrew; Dungarani, Priya; Ulysse, Guerlain; Kochhar, Kanika; Vidri, Boris; Strait, Kelsey; Jourdian, George; Xiang, Zuoshuang
Vaccine Investigation and Online Information Network
database
summary
VIPERdb
Reddy, Vijay; Montiel-Garcia, Daniel; Santoyo-Rivera, Nelly; Ho, Phuong; Carrillo-Tripp, Mauricio; Brooks, III, Charles; Johnson, Jack
VIrus Particle ExploreR data base
database
summary
ViPR
Pickett, Brett; Sadat, Eva; Zhang, Yun,; Noronha, Jyothi; Squires, Richard; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larsen, Christopher; Dietrich, Jon; Klem, Ed; Scheuermann, Richard
Virus Pathogen and analysis Resource
database
summary
Vir-Mir db
Prediction of viral microRNA candidate hairpins
database
summary
Viral Bioinformatics Resource
Upton C.
and Lefkowitz E.J.
Viral genomes, orthologous genes and gene families
database
summary
Viral Genomes
Eneida L. Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Obichuck, Alejandro A. SchÃƒÂ¤ffer and J. Rodney Brister
Nucleotide and protein sequences of viral reference genomes
database
summary
ViralORFeome (discontinued)
J. Pellet, L. Tafforeau, M. Lucas-Hourani, V. Navratil, L. Meyniel, G. Achaz, A. Guironnet-Paquet, A. Aublin-Gex, G. Caignard, P. Cassonnet, A. Chaboud, T. Chantier, A. Deloire, C. Demeret, M. Le Breton, G. Neveu, L. Jacotot, P. Vaglio, S. Delmotte, C. Gautier, C. Combet, G. Deleage, M. Favre, F. Tangy, Y. Jacob, P. Andre, V. Lotteau, C. Rabourdin-Combe, and P. O. Vidalain
A reference collection of viral ORFs and their clones
database
summary
ViralZone
Le Mercier, philippe; De Castro, Edouard; Hulo, Chantal; Masson, Patrick; Auchincloss, Andrea; Bridge, Alan J
ViralZone 2024 provides higher-resolution images and advanced virus-specific resources.
database
summary
ViralZone
Chantal Hulo
, Edouard de Castro
, Patrick Masson
, Lydie Bougueleret
,Amos Bairoch
2,3
, Ioannis Xenarios
1,4
and Philippe Le Mercier
Molecular and epidemiological information on viral genera and families
database
summary
ViRBase
Wang, Dong; Cheng, Jun; Lin, Yunqing; Xu, Linfu; Chen, Chenke; Kang, Juanjuan; Cui, Tianyu; Li, Qi; Xu, Kaixin; Ning, Lin; Huang, Yan; Zhao, Xiaoyang; Su, Xi; Li, Yan- Hui; Yang, Bin
ViRBase v3.0: a virus and host ncRNA-associated interaction repository with
database
summary
ViRBase
Yanhui Li; Changliang Wang; Zhengqiang Miao; Xiaoman Bi; Deng Wu; Nana Jin; Liqiang Wang; Hao Wu; Kun Qian; Chunhua Li; Ting Zhang; Chunrui Zhang; Ying Yi; Hongyan Lai; Yongfei Hu; Lixin Cheng; Kwong-Sak Leung; Xiaobo Li; Fengmin Zhang; Kongning Li; Xia Li; Dong Wang
Virus-host interaction-associated ncRNA
database
summary
VIRE
Suguru Nishijima; et al.
VIRE: a metagenome-derived, planetary-scale virome resource with environmental and host metadata
database
summary
VirHostNet
Guirimand, Thibaut; Delmotte, StÃƒÂ©phane; Navratil, Vincent
A knowledgebase of virus-host molecular interaction networks
database
summary
VirJenDB
Noriko Cassman; et al.
VirJenDB: A FAIR (meta)data and bioinformatics platform for all viruses
database
summary
ViroidDB
Lee, Benjamin; Neri, Uri; Oh, Caleb; Simmonds, Peter`; Koonin, Eugene
Viroids and viroid-like circular RNA agents
database
summary
VirOligo
Onodera K., Song Y. and Melcher U.
Virus-specific oligonucleotides for PCR and hybridization
database
summary
VIRsiRNAdb
Manoj Kumar
Experimentally validated Viral siRNA/shRNA
database
summary
Virus Mentha
Calderone, Alberto; Licata, Luana; Cesareni, Gianni
Virus-host protein interactions
database
summary
Virus Taxonomy
Lefkowitz, Elliot; Dempsey, Donald; Hendrickson, Robert; Orton, Richard; Smith, Donald
No description supplied
database
summary
ViruSurf
Arif Canakoglu
, Pietro Pinoli
, Anna Bernasconi
, Tommaso Alfonsi
, Damianos P. Melidis
and Stefano Ceri
Integrated database to investigate viral sequences
database
summary
VISTA Enhancer Browser
Visel A.
, Minovitsky S.
, Dubchak I.
1,2
and Pennacchio L.A.
1,2
Enhancer elements in the human genome
database
summary
ViTa
microRNAs targets of the influenza virus
database
summary
VKCDB - Voltage-gated K
Channel Database
Voltage-gated potassium channel database
database
summary
Voronoia
A database for the computation of atomic packing density values of protein structures
database
summary
Voronoia4RNA
Jochen Ismer
Packing of RNA molecules and complexes
database
summary
VThunter
Chen, Dongsheng; Tan, Cong; Ding, Peiwen; Luo, Lihua; Zhu, Jiacheng; Jiang, Xiaosen; Ou, Zhihua; Ding, Xiangning; Lan, Tianming; Zhu, Yixin; Jia, Yi; Wei, Yanan; Li, Runchu; Qin, Qiuyu; Sun, chengcheng; Zhao, Wandong; Lv, Zhiyuan; Wang, Haoyu; Wu, Wendi;
scRNA-seq-based analysis of virus receptor expression across animals
database
summary
WALTZ-DB
Nikolaos Louros, Katerina Konstantoulea, Matthias De Vleeschouwer, Meine Ramakers, Joost Schymkowitz, Frederic Rousseau
The Switch Lab introduces WALTZ-DB 2.0, an open-access database containing
database
summary
WDCM
Ma, Juncai; Wu, Linhuan; Sun, Qinglan; DESMETH, Philippe; Sugawara, Hideaki; McCluskey, Kevin; Smith, David; Alexander, Vasilenko; Lima, Nelson; Ohkuma, Moriya; Robert, Vincent; Zhou, Yuguang; Li, Jianhui; Fan, Guomei; Ingsriswang, Supawadee; Ozerskaya, Svetlana
World Data Center of Microorganisms collections
database
summary
WDDD - Worm Developmental Dynamics Database
Kyoda, K.
1,2,3
, Adachi, E.
2,3
, Masuda, E.
, Nagai, Y.
, Suzuki, Y.
, Oguro, T.
, Urai, M.
, Arai, R.
, Furukawa, M.
, Shimada, K.
, Kuramochi, J.
, Nagai, E.
, and Onami, S.
1,2,3,4,5,6
Worm Developmental Dynamics Database
database
summary
WDSPdb
Wu, Yun-dong; Wang, Yang; Hu, Xue-Jia; Zou, Xu-Dong; Wu, Xian-hui; Ye, Zhi -Qiang
WD40 domain structure predictions
database
summary
WebGeSTer DB
Anirban Mitra
, Anil K. Kesarwani
, Debnath Pal
and Valakunja Nagaraja
1,3
Genome Scanner for bacterial transcriptional Terminators
database
summary
webTWAS
Cao, Chen; Wang, Jianhua; Kwok, Devin; Zhang, Zilong; Cui, Feifei; Zhao, Da; Jun Li, Mulin; Zou, Quan.
Transcriptome-Wide Association Studies
database
summary
WeGET
Szklarczyk, Radek; Megchelenbrink, Wout; Cizek, Pavel; Ledent, Marie; Szklarczyk, Damian; Velemans, Gonny; Huynen, Martijn
Weighted gene co-expression tool
database
summary
WERAM
Xue, Yu; Xu, Yang,'; Zhang, Shuang; Lin, Shaofeng; Guo, Yaping; Deng, Wankun; Zhang, Ying.
Writers, Erasers and Readers of Histone Acetylation and Methylation
database
summary
wFleaBase
Gilbert, D.G. and Colbourne, J.K.
Genome database of the eco-genetic model organism waterflea,
Daphnia pulex
database
summary
WholeCellKB - Model Organism Databases for Comprehensive Whole-Cell Models
Karr, J.R.
, Sanghvi, J.C.
, Macklin, D.N.
, Arora, A.
and Covert, M.W.
An integrated pathway/genome database for whole-cell modeling
database
summary
WikiPathways
Thomas Kelder
Wiki for curation of biological pathways
database
summary
WikiPathways
Kutmon, Martina; Martens, Marvin; Ammar, Ammar; Riutta, Anders; Waagmeester, Andra; Slenter, Denise; Hanspers, Kristina; Miller, Ryan; Digles, Daniela; Lopes, Elisson; Ehrhart, Friederike; Dupuis, Lauren; Winckers, Laurent; Coort, Susan; Willighagen, Egon
WikiPathways (wikipathways.org) captures the collective knowledge represent
database
summary
WikiPathways
Pico, Alex; Agrawal, Ayushi; Balci, Hasan; Hanspers, Kristina; Coort, Susan; Martens, Marvin; Slenter, Denise; Ehrhart, Friederike; Digles, Daniela; Waagmeester, Andra; Wassink, Isabel; abbassidaloii, t; Lopes, Elisson; Iyer, Aishwarya; Acosta, Javier; Willighagen, Lars; Nishida, Kozo; Riutta, Anders; Basaric, Helena; Evelo, Chris; Willighagen, Egon; Kutmon, Martina
WikiPathways 2024: next generation pathway database
database
summary
WITHDRAWN
preissner, robert; Gallo, Kathleen; Goede, Andrean; Eckert, Andreas; Gohlke, BjÃ¶rn
Withdrawn 2.0 - update on withdrawn drugs with pharmacovigilance data
database
summary
WITHDRAWN
preissner, robert; Gallo, Kathleen; Goede, Andrean; Eckert, Andreas; Gohlke, BjÃ¶rn
Withdrawn 2.0 - update on withdrawn drugs with pharmacovigilance data
database
summary
Wnt Database
Nusse R.
Wnt proteins and phenotypes
database
summary
WorfDB - Worm ORF Database
Predicted proteins from C. elegans
database
summary
WormBase
Lee, Raymond; Howe, Kevin; Harris, Todd; Valerio, Arnaboldi; CAin, Scott; Chan, Juancarlos; Chen, Wen; Davis, Paul,; Gao, Sibyl; Grove, Christian; Kishore, Ranjana; MÃƒÂ¼ller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael.; Raciti, Daniela; Rodgers, Faye; Russell, Matthew; Schindelman, Gary; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Qinghua; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matt; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul
WormBase (http://www.wormbase.org) is an important knowledge resource for b
database
summary
WormBook
Girard, L.
, Fiedler, T.
, Harris, T.
, Carvalho, F.
, Antoshechkin, I.
, Han, M.
, Sternberg, P.
, Stein, L.
and Chalfie, M.
Peer-reviewed chapters on the biology of
C. elegans
database
summary
WormQTL
Morris Swertz
Natural variation data in Caenorhabditis spp.
database
summary
WormQTLHD
Swertz, Morris; van der Velde, Kasper; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, Basten; Kammenga, Jan; Jansen, Ritsert; Li, Yang
Links from human disease to natural variation data in C. elegans
database
summary
X:MAP
Annotation and visualization of genome structure for Affymetrix exon array analysis
database
summary
XenBase
Karpinka, J; Fortriede, Joshua; Burns, Kevin; Ponferrada, Virgilio; James-Zorn, Christina; Lee, Jacqueline M; Karimi, Kamran; Zorn, Aaron; Vize, Peter
Xenopus
genomics resource
database
summary
Xenbase
Karimi, Kamran; Fortriede, Joshua; Lotay, Vaneet; Burns, Kevin; Wang, Dong; Fisher, Malcolm; Pells, Troy; James-Zorn, Christina; Wang, Ying; Ponferrada, Virgilio; Chu, Stanley; Chaturvedi, Praneet; Zorn, Aaron; Vize, Peter
No description supplied
database
summary
xQTLatlas
Tianyi Zhao
xQTL at cellular resolution
database
summary
XTalkDB
Sam, Sarah; Teel, Joelle; Tegge, Allison; Bharadwaj, Aditya; Murali, T. M.
Crosstalk among signaling pathways
database
summary
yApoptosis
Wanichthanarak K, Cvijovic M, Molt A, Petranovic D.
yeast apoptosis database
database
summary
YDPM - Yeast Deletion Project
Yeast deletion project and mitochondria database
database
summary
Yeast Intron Database
Telerski, A.
, Centers, R. J.
, Ares, M.
Splicesomal introns in
Saccharomyces cerevisiae
database
summary
Yeast Resource Center
Yeast resource center public data repository
database
summary
Yeast snoRNA Database
Yeast small nucleolar RNAs
database
summary
YeastNet
Lee, Insuk; Kim, Hanhae; Shin, Junha; Kim, Eiru; Kim, Hyojin,; Shim, Jung
Functional gene networks for Saccharomyces cerevisiae
database
summary
YEASTRACT
Teixeira M.C.
1,3
, Monteiro
, Jain P.
, Tenreiro S.
1,3
, Fernandes A.R.
1,3
, Mira N.
1,3
, Alenquer M.
1,3
, Freitas A.T.
2,3
, Oliveira A.L.
2,3
and SÃƒÆ’Ã‚Â¡-Correia I.
1,3
Yeast transcriptional regulation
database
summary
YEASTRACT
SÃƒÂ¡-Correia, Isabel; Teixeira, Miguel; Monteiro, Pedro; Palma, Margarida; Costa, Catarina; Godinho, ClÃƒÂ¡udia; Pais, Pedro; Cavalheiro, Mafalda; Antunes, Miguel; Lemos, Alexandre; Pedreira, Tiago
No description supplied
database
summary
YEASTRACT+
Monteiro, Pedro ; Teixeira, Miguel; Viana, Romeu; Palma, Margarida; Oliveira, Jorge; Galocha, MÃ³nica; Mota, Marta; Couceiro, Diogo; Galhardas, Maria; Antunes, Miguel; Costa, InÃªs; Pais, Pedro; Parada, Carolina; Chaouiya, Claudine; SÃ¡-Correia, Isabel
YEASTRACT+: a portal for the exploitation of global transcription regulatio
database
summary
YeTFaSCo
Carl de Boer
Yeast Transcription Factor binding Site sequence Collection
database
summary
YGOB
Byrne K.P. and Wolfe K.H.
Yeast Gene Order Browser
database
summary
YH database
A database for the first Asian diploid genome
database
summary
YM500
Cheng, Wei-Chung; Chung, I-Fang; Tsai, Cheng-Fong; Huang, Tse-Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting-Yu; Sun, Hsing-Jen; Chao, Jeffrey Yung-Chuan; Cheng, Cheng-Chung; Wu, Cheng-Wen; Wang, Hsei-Wei
smRNA-seq database for miRNA research
database
summary
YMDB
David Wishart
Yeast Metabolome Database
database
summary
yMGV - Yeast microarray global viewer
Yeast expression data
database
summary
YPA
Darby Tien-Hao Chang, Cheng-Yi Huang, Chi-Yeh Wu, and Wei-Sheng Wu
Yeast Promoter Atlas
database
summary
ZEBRA
Kern, Fabian; Flotho, Matthias; Amand, JÃ©rÃ©my; Hirsch, Pascal; Grandke, Friederike; Wyss-Coray, Tony; Keller, Andreas
ZEBRA: A hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution
database
summary
ZFIN
Howe, Douglas; Ramachandran, Sridhar; Bradford, Yvonne; Fashena, David; Toro, Sabrina; Eagle, Anne; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Taylor, Sierra; Paddock, Holly; Pich, Christian; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; van Slyke, Ceri; Westerfield, Monte
The Zebrafish Information Network
database
summary
zfishbook
Stephen C Ekker
Transposon-labeled mutants in zebrafish
database
summary
ZiFDB
Voytas, D., and Fu, F.
Zinc Finger DataBase
database
summary
ZInC
Shawn Burgess
Zebrafish Insertions Collection
database
summary
ZOVER
Yang, Jian; Zhou, Siyu,; Liu, Bo `; Han, Yelin; Wang, Yuyang; Chen, Lihong,; Wu, Zhiqiang
Zoonotic and vector-borne viruses
database
summary
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Category/Paper List
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