Extended Data Fig. 7: Properties of invariant enhancer–promoter interactions.

a, Metaplot showing average ratio of enhancer interaction frequency between active and inactive tissues for invariant (interactions present in all 7 main tissues: brain, face, limb, heart, neural tube, trunk and tail, n = 171) and tissue-specific ( ≤ 6 main tissues, n = 775) interactions. Light blue/orange shading indicates 95% confidence intervals estimated by non-parametric bootstrapping. 10 kb upstream and downstream of enhancer bait and target promoter are also indicated (grey bar). b, The average ratio of invariant enhancer-promoter interaction frequency between active and inactive tissues for enhancers active in the brain, face, limb, heart and neural tube E–P. Data is shown only for tissues with at least 20 active enhancers that form invariant E–P interactions. P values were calculated by paired-sample two-sided Wilcox test and adjusted for multiple testing. c, The number of tissues in which enhancers forming invariant (10 tissues, n = 98) or tissue-specific ( ≤ 4 tissues, n = 196) E–P interactions are active in vivo. d, The average phyloP scores of enhancers forming invariant (10 tissues, n = 98) or tissue-specific ( ≤ 4 tissues, n = 196) E–P interactions. P values in panels c and d were calculated by two-sided Wilcox test. e, Gene Ontology enrichment for genes that form invariant (10 tissues) E–P interactions (Biological process and Molecular function). Q values were calculated by over-representation test and adjusted for multiple testing. For the boxplots in panels b-d, the central horizontal lines are the median, with the boxes extending from the 25th to the 75th percentiles. The whiskers further extend by ±1.5 times the interquartile range from the limits of each box.