(A) Association of shared TFs in CRMs and Singletons with human gene expression obtained by RNA-seq in human liver (Kutter et al., 2011; E-MTAB-424). TFs in CRMs or Singletons were assigned to the nearest gene, and the FPKM (Fragments Per Kilobase of exon per Million reads) was recorded. In contrast to Singletons, TFs in Deeply CRMs are associated with highly expressed genes (adjusted p-values shown). The numbers of target gene associations for the singletons and CRMs in categories 1 to 5 are: 19354(S), 32706(CRM); 6325(S), 14669(CRM); 1935(S), 5755(CRM); 1005(S), 3292(CRM); and 459(S), 2530(CRM). (B) Comparison with CRMs and Singletons to a reference mRNA-seq data from 16 human tissues (E-MTAB-513) further shows that relative to singletons, liver-specific CRMs are highly expressed in liver, and that each TF contributes to this specificity. The number of gene associations for each category in the liver data is shown in white text within the heat map.