…provided in Additional File 3 , which is a .cdt file that can be opened in Java Treeview for flexible browsing. To estimate the number of genes significantly affected by the pH effect, we used the Nearest Shrunken Centroids classifier [ 25 ] to calculate the cross-validation erro…

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… was used to perform k-means clustering with Euclidean distance metric and Java TreeView 36 was used for visualization. The H3K27ac signal in the heatmap represents the IP signal minus input for a +/− 1500bp window around the peak signal of each enhancer. Clusters of enhancers sp…