Fig. 2

Properties of predicted intergenic enhancers. Relative enrichment of PU.1 (a), DNaseI (b) and polyadenylated long (>200 nt) nuclear RNA (c) at active and silent enhancers, as well as for regions of no-change in chromatin. The violin plots describe the distributions for the z-score of the relative enrichment along the y-axis. Positive z-score values mean enrichment in K562, while negative z-scores mean enrichment in GM12878. d Percentage of enhancers at a given distance from the TSS, for active (blue), silent (green), as well as for the corresponding randomized sets (red and cyan) (Methods). e Relative expression change in genes associated to enhancers by proximity to the TSS. The violin plot describes the distributions of z-scores of the relative enrichment of RPKM values along the y-axis for genes associated to active and silent enhancers, as well as for no-change regions calculated with Pyicoteo [23]. Genes where linked to the nearest enhancers within a distance range between 2 and 10 kb. f Cumulative distribution of enhancer nearby genes related to cancer in terms of the distance between the TSS and the closest enhancer. The comparison is made between active and silent predicted enhancers, and the corresponding randomizations