Fig. 2

Differential enhancer and promoter enrichments for differential expression across conditions and cell types. a Schematic depicting a simplified version of the enrichment analysis test results shown in b. Any diff-CRE was counted as a “success” overlap in the hypergeometric enrichment test for a given context if it had a target gene that was DE in that context. Color gradients illustrate that each element has a directionality, which is the subject of analysis in c and d. b Results of one-sided Fisher’s exact tests for DE gene enrichment in diff-CREs are shown as odds ratios plotted against significance. Vertical dotted lines mark an odds ratio of 1 and horizontal dotted lines mark the Bonferroni-corrected P-value threshold. Points above this significance threshold are labeled with their context (see table inset). Score types used to define diff-CREs in each test are indicated by the shape and color of the points. c Schematic depicting the enrichment analysis test results shown in d. Each element from any overlap in a (e.g., gray gradient callout) was split into AFR- and EUR-biased directionality and any diff-CRE with a DE target gene in each context was counted as a “success” overlap if the ancestry DE direction matched the diff-score direction of the CRE (e.g., higher expression and higher score in AFR (blue)). For diff-CREs with multiple DE target genes, these targets were required to match direction to be included in each test. d Results of one-sided Fisher’s exact tests for diff-CRE matching DE directionality are shown as odds ratios plotted against significance. Vertical dotted lines mark an odds ratio of 1 and horizontal dotted lines mark the Bonferroni-corrected P-value threshold. Points above this significance threshold are labeled with their context. For a more detailed illustration of these tests, see Additional file 1: Fig. S13a,c