Summary of Pan-cancer Sample Groups and alignments with clinical features.

A: Combinatorial expression patterns of 18 Gene Groups (rows) in 228 Sample Groups (columns). The three Meta Gene Groups are marked on the left: Meta Gene Group 1 (immune and inflammatory responses, red), Meta Gene Group 2 (embryonic development and neurogenesis, green), Meta Gene Group 3 (cell cycle process and DNA repair, blue). Sample Groups are sorted by the combinatorial expression patterns of Meta Gene Groups. The 8 Pan-cancer Sample Groups (0–7) are marked on the top and separated by yellow vertical lines. A white patch indicates that a Gene Group is not enriched in any Super Module in the cancer types of a Sample Group. B: Expressions of 16860 genes in 11701 samples. Genes are sorted by Gene Groups, and Meta Gene Groups are marked on the left. Samples are sorted by Sample Groups and Pan-cancer Sample Groups. Gene Groups and Pan-cancer Sample Groups are separated by yellow boundaries. The Pan-cancer Sample Groups (prototypes), cancer types, sample purity, DNA and RNA stemness of samples are displayed on the top. C: mRNA expressions of three Meta Gene Groups overlaid with several pan-cancer features in seven cancer types. Samples within each cancer type are sorted by Sample Groups. The following sample features are also displayed: cancer types, prototypes (Pan-cancer Sample Groups), sample purity, DNA and RNA stemness, mesenchymal states, hyper-mutated states, and mutations of selected genes. Prototype color codes follow the top row in panel B. D: Direction and strength of mRNA expression-survival time associations (pdiff scores of Cox regression coefficient distributions) of all Gene Groups in all cancer types. Positive and negative deviations (indicating positive and negative Cox regression coefficients) have red and green colors respectively.