Fig. 7

Common and cell-type-specific regulatory modules. a RMD was applied to ChIP-seq binding sites of 56 TFs in human K562 cells and GM12878 cells. Each cell in the heatmap represents the z-score of TF binding site count (standardized along the columns) of a TF (column) in a module (row). The bottom bar plot shows the total number of binding sites of the TFs. The right bar shows the percentage of the sites contributed from K562 data for the modules. The top and left dendrograms were computed by applying hierarchical clustering on the regulatory module matrix with Pearson correlation distance and average linkage. b A scatter plot showing that the cell-type-specific modules are preferentially used in the differentially bound regions in K562 cells and GM12878 cells. c Distinct cell-type-specific modules are used in the same genomic regions in different cell types. A set of 1956 regions that are bound by K562 enhancer module factors in K562 (left panel) and by GM12878 enhancer module factors in GM12878 cells (right panel). The TFs are in the same order as in a