Fig. 3
Genomic characterization of common super-enhancer domains. a Boxplots of correlation between log2(H3K27ac RPM + 1) in super-enhancer domains and RPKM of putative target genes (n = 1208 for common SE domains, n = 3733 for non-unique SE domains, n = 1098 for unique SE domains). Pearson correlation coefficient was calculated for each super-enhancer domain across 24 cell/tissue types. Significance of difference between super-enhancer domain categories was evaluated by KS test (*** p-value < 5 × 10− 12). b An example of common super-enhancer domain showing high H3K27ac signal across cell/tissue types but showing irregular RNA expression level. Left panel presents genome browser snapshot of H3K27ac signals at super-enhancer domain. Right panel presents RNA-seq RPKM of MLL5 gene. Pearson correlation coefficient (PCC) between H3K27ac signal at a super enhancer domain and the MLL5 RPKM is shown below. c Boxplots of mean sequence conservation score for each super-enhancer domain (n = 1098 for unique SE domains, n = 3733 for non-unique SE domains, n = 1208 for common SE domains). Significance of difference between super-enhancer domain categories was evaluated with KS test (*** p-value < 1.1 × 10− 5 between random and others, p-value < 5.1 × 10− 12 for the rest). d Boxplots of mean CDTS for each super-enhancer domain (n = 1098 for unique SE domains, n = 3733 for non-unique SE domains, n = 1208 for common SE domains). Significance of difference between super-enhancer domain categories is evaluated with KS test (*** p-value < 1.7 × 10− 9 for unique and random, p-value < 3.0 × 10− 14 for the rest). e An example of adjacent non-unique super-enhancer domain and common super-enhancer domain illustrating evolutionary conservation of common super-enhancer domain. Shown together are 100-way PhastCons and CDTS. 100-way PhastCons track has the scale from 0 to 1, and CDTS track is scaled from − 20 to + 20. Common and unique super-enhancer domain are shown as right and left bar, respectively, in ‘Super-enhancer domains’ annotation