Fig. 3

Heat maps of signals of the four epigenetic marks around the positive sets CRM+TF⁺ and CRM+S⁺, and the negative sets non-CRM and CRM+S⁻ in the HCT116 cells. We plotted signals of CA, H3K27ac, H3K4me1, and H3K4me3 around the sequences in each set. To make the density plots, we first extended the centers of sequences to 10 kb, and then for each 100-bp tiling window in the extended regions, we calculated the signal scores using EnrichedHeatmap (w0 mode) [76]. Note that the scales of vertical axes of the density plots on the top of heat maps are different in the right and left panels. The sequences in each set are sorted in the descending order of the CA signals for all the marks