For motif search (see below), we identified the set of robust enhancers that were significantly deviating between facets using Kruskal-Wallis rank sum tests (Benjamini-Hochberg FDR < 0.05) and performed pair wise post-hoc tests (Nemenyi-Damico-Wolfe-Dunn (NDWD) test59,60 using the R coin package61 to identify enhancers with significant differential expression (Bonferroni single-step adjusted P < 0.05) between facets. Cell type facets and tissue/organ facets were analyzed separately. Each enhancer was considered differentially expressed in a facet with at least one pair-wise significant differential expression and overall positive standard linear statistics. This procedure means that we, for each robust enhancer, selected the facets, if any, with strong overall differential expression compared to all other facets. It should be noted that differential expression in this sense is not equivalent to facet-specific (exclusive) expression.
