Figure 1

Refinement of TFBS data to final network. The original REMAP (v1.2) data contain 80,129,424 TFBS. These data were first filtered to keep only those found in CRMs (regions where TFBS were found to overlap). These peaks were then assigned to TSS of all genes as annotated in Ensembl 89 in a window of 50 kb upstream of the TSS and 10 kb downstream of the TSS (see “Methods”). To increase the confidence in the interactions between TFs and target genes, TSS-TF interactions were filtered based on the mean binding profiles of each TF. Interactions ≥ mean binding were maintained. This filtering produces the final network. As all interactions in which we are interested contain feedback, we produced a trimmed network that only contains genes which are both targets and regulators.