FIGURE 2 from Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell–intrinsic Stemness or Mesenchymality Characteristics

EMT-related signatures and their associations with cancer pathways or processes. We studied 11 mesenchymal, EMT, and stemness signatures and their relation to other biological processes in TCGA cancer patients and CCLE cancer cell lines. Left heat maps: Gene expression signature scores of coherent signatures and their correlation with sample purity (CPE) in TCGA colorectal cancer (CRC) samples. The heat maps have been supplemented with single gene marker expression. The column annotation lists important markers for mesenchymal (VIM) and epithelial (EPCAM, CDH1) properties. Samples from left to right have decreasing levels of VIM expression, and signatures groups have an increasing correlation with tumor purity from bottom to top. Light gray areas indicate signatures that did not satisfy the coherence scoring threshold. Right heat maps: An analogous analysis as in colorectal cancer to the left, here for TCGA HNSC samples.