Fig. 3

Functional pathways, mutation genes, tumor heterogeneity, tumor stemness and TME evaluation between two subtypes. A. Waterfall plot showing the top 10 most commonly mutated genes between two subtypes; B, C. the functional differences between two subtypes using GSEA; D. the differences of tumor heterogeneity and tumor stemness between two subtypes; E. the differences of tumor immune microenvironment scores and infiltrating cells between two subtypes. TMB = tumor mutation burden; MATH = mutant allele tumor heterogeneity; MSI = microsatellite instability; HRD = homologous recombination deficiency; LOH = loss of heterozygosity; DMPss = differentially methylated probes-based stemness scores; DNAss = DNA methylation-based stemness scores; ENHss = enhancer elements/DNA methylation-based stemness scores; EREG.METHss = epigenetically regulated DNA methylation-based stemness scores; EREG.EXPss = epigenetically regulated RNA expression-based stemness scores; RNAss = RNA expression-based stemness scores. TIDE = Tumor Immune Dysfunction and Exclusion