Fig. 2: Immune system-related correlates of patient survival.
a TCGA tumor mRNA expression profiles were separately scored for each of 24 gene expression-based signatures of immune cell infiltrates41, with 11 signatures associating with patient survival in pan-cancer analyses (FDR < 5%, nominal p < 0.01, Cox correcting for cancer type). For top immune signatures, heat maps represent the respective associations with patient survival for each individual cancer type. T helper 2 cells not represented here, as the genes in this signature appeared not specific to T cells41. b Across the TCGA pan-cancer cohort, associations with patient OS of the macrophage mRNA signature (top) and the T cell mRNA signature (bottom). Stratified log-rank p values correct for cancer type. c Diagram of immune checkpoint pathway5 (featuring interactions between T cells and antigen-presenting cells, including tumor cells), with significant pan-cancer mRNA associations with patient survival indicated (Red, higher with worse survival; Blue, higher with better survival; Cox correcting for cancer type). d Similar to part (b), but for immune cell types and their associated markers46 (left) and tumor-associated macrophage roles in the tumor microenvironment44 (right). Genes with CNA associated with survival (p < 0.05, Cox correcting for cancer type) in the same direction as the mRNA association are highlighted using gold rectangles. Genes with CGI associated with survival (p < 0.05, Cox correcting for cancer type) in the opposite direction from the mRNA association are highlighted using purple rectangles. e The macrophage signature and the T cell signature from part (a) were separately applied to eight independent gene expression datasets outside of TCGA (from Fig. 1f). For four datasets, the macrophage signature was associated with worse survival, while for the other four datasets, the T cell signature was associated with better survival.
