Fig. 2

Tissue-specific enhancers are associated with tissue-specific and tissue-shared promoters. a Within each species, promoter activity and gene expression were distributed between tissue-specific and tissue-shared, while enhancer activity was mostly tissue-specific (see Additional file 1: Figure S5). The bars are a summation of numbers across all ten study species while and the pie charts show the portions of tissue-shared (across any two tissues) and tissue-specific regions split by testis-specific and somatic-specific; mouse as a representative species is shown in Additional file 1: Figure S6A. b Numbers of tissue-shared (y-axis) and tissue-specific (x-axis) enhancers associated with each active promoter are shown for the four tissues. The schematic (right) represents two extreme examples: promoters predominantly associated with tissue-shared enhancers (top) or tissue-specific enhancers (bottom). Tissue-shared promoters (left panels) are associated with a higher ratio of tissue-shared versus tissue-specific enhancers; whereas tissue-specific promoters (right panels) are predominantly associated with tissue-specific enhancers. A linear regression was fitted to the ratio of tissue-specific to tissue-shared enhancers per promoter and is shown as a line. For a distribution of all the tissue-specific to tissue-shared ratios see Additional file 1: Figure S6B. c Observed expression changes between tissues for genes associated with regulatory regions in muscle, brain, and testis. The plots show the distribution of differential expression with liver as a reference (DESeq2 adjusted p value < 0.05), of genes nearest to 4-tissue-shared regulatory regions and tissue-specific regulatory regions (p values calculated using one sided Wilcoxon test; tissue-specific expression change is greater than tissue-shared)