Fig. 6

Enrichment of oncogenes, TSGs, and DRGs in modules and PAM50 gene cardinality. a Barplot showing the fraction (pink color) of oncogenes, tumor suppressor genes, or dual role genes encompassed by co-expression modules. Modules without any annotated cancer genes are not included, neither is the gray module of genes (genes not found to be co-expressed). Plus signs indicate that a module was significantly enriched for oncogenes, TSGs, or DRGs, while minus signs indicate that the module was significantly depleted of these. b Tile plot showing the expression cardinality of PAM50 genes from the analysis compared with the literature. Orange (up) and green (down) colors denote the directionality of genes from the literature for each subtype. Colors dark gray, light gray, and white indicate if a gene was found to be differentially expressed in the current analysis. Light blue and white show the consensus of expression cardinality for a given PAM50 gene between the literature and current analysis. Dots below the tiles highlight which of the PAM50 genes are annotated in the COSMIC Cancer Gene Census set and in the CancerMine database (filtered, see the “Materials and methods” section)