Figure 3

Higher peaks overlap more and have more consistent support in other data marking regulatory regions. Peaks in K562 for each TF (panel columns) were binned in 10 equally-sized groups with increasing peak height (ordered along x-axis) and the average values for different genomic characteristics (panel rows) were computed for each group (y-axis). From top to bottom row, the genomic characteristics are: “HeLa-S3”: percentage of peaks in K562 that overlap with a peak in HeLa-S3.; “Promoter”: percentage of peaks that overlap with promoter regions.; “CpG rich”: percentage of peaks that overlap with CpG-rich regions.; “DNase”: average count of DNase-seq reads in peak region—a measure of chromatin accessibility.; “H3K4me3”: average count of H3K4me3 ChIP-seq reads in a peak region—a measure of chromatin activity.; “phyloP”: average phyloP scores in peak region for a 28-way placental mammals multiple alignment—a measure of sequence conservation.; “PWMscore”: average maximal PWM score in peak region (where available).; “ClusterTF”: average number of peaks in peak cluster. See Methods section for definition of promoters, CpG-rich regions, and clusters and for details on other genomic data. The blue line in each panel is a linear regression line between peak height bin and genomic characteristic; the dark gray areas surrounding these lines are 95% confidence intervals; blue stars mark significant regression line slopes (p ≤0.05).