PPI and transcriptional sub-networks in breast tumors. (A) The E2F and NFY expression modules and an overlapping PPI sub-network. (B) The ETS, IRF, NFκ B, and Runx expression modules and an overlapping PPI sub-network. For clarity, we displayed nodes which have more than one links. Red, yellow and blue nodes denote transcriptional regulators, regulated genes, and their interacting partners, respectively. Red links denote transcriptional regulations predicted by our analysis, and blue links denote PPIs registered in the HPRD.