Schematic of module detection method based on TF interactions. Based on gene expression profiles across different tissues, we identified groups of genes that are preferentially expressed in tissues (e.g. gene C and D in the schematic). For each group of genes, we searched the binding sites of known TFs in promoter regions and determined the TF pairs whose binding sites tend to co-occur in close proximity. A tissue-specific TF interaction network was obtained from the analysis. We then scanned the genomic regions and identified cis-regulatory regions (CRMs). The CRMs are defined as regions enriched with TF interactions. Note the first steps were implemented in our previous work  while this paper focuses on the last step.