PID pathway-pathway relationships discovered in NMF features constructed from the TCGA pan-cancer gene expression dataset. a Pathways in this module are responsible for cell cycle progression. b Wnt signaling interactions with nuclear Beta-catenin signaling, FGF signaling, and BMP signaling have all been linked to cancer progression. c Here, we observe functional links between pathways responsible for angiogenesis and those responsible for cell proliferation. d The VEGF-VEGFR pathway interacts with the S1P3 pathway through Beta3 integrins. e This module contains many relationships related to immune system processes. The interaction cycle formed by T-Cell Receptor (TCR) signaling in naïve CD4+ T cells and IL-12/IL-4 mediated signaling events, outlined in yellow, is one well-known example. The cycle in blue is formed by the ATF2, NFAT, and AP1 pathways; pairwise co-occurrence of these three transcription factor networks may suggest that dysregulation of any one of these pathways can trigger variable oncogenic processes in the immune system. The list of PID pathway-pathway relationships visualized in the network is available as an Additional file 3 for this paper.