Figure 2

Explaining regions of increased peak overlap and TF expression difference. A) Relative overlap (see Figure1C) of peaks mapping to promoter regions compared with other peaks. Peaks in promoter regions overlap more than peaks in other genomic regions. B) Relative overlap of peaks in promoters of housekeeping genes (list from[39]) compared with peaks in other promoters. Peaks in promoters of housekeeping genes overlap more than peaks in promoters of other genes. C) Relative overlap of peaks in CpG-rich promoter regions compared with peaks in CpG-poor promoter regions. D) Alternative local binding sites. The y-axis shows the number of K562 peaks that overlap with a peak in HeLa-S3 when, one by one, each given peak region in K562 is extended by 0, 500, 1,000, 4,000 and 10,000 bp (half to each side of the peak). The number of overlaps does not increase markedly when considering larger regions surrounding the peaks. E) TF expression difference between cell types versus TF peak count difference between cell types. The x-axis gives the difference in number of ENCODE Caltech paired-end RNA-seq reads mapping to a TF gene in K562 versus HeLa-S3 (see Methods). The y-axis gives the difference in number of peaks regions in K562 vs HeLa-S3. Both differences were normalized to the range {-1, 1}. P-values for t-tests on slope of linear regression lines are shown with all TFs included (dashed line; p = 0.2) and without the expression outliers c-Fos and c-Myc (dotted line; p = 7.2∗10⁻³).