Fig. 2

Cancer-specific relative enrichment of mutations in T cell-inflamed and non-T cell-inflamed tumors from all protein-coding genes on the genome. a Each tumor type shows a set of gene mutations enriched in T cell-inflamed or non-T cell-inflamed tumor group. Stars label the four representative tumor types in b. b Cancer-specific mutated genes that are preferably mutated in T cell-inflamed tumors (yellow) or non-T cell-inflamed tumors (blue) in four select tumor types. Coefficients of “mutation status” term from logistic regression models are shown on the x-axis, which describe the association between mutation status and tumor groups in the unit of logits. P values are shown on the y-axis. Individual genes of interest discussed in the main text were labeled in bold. The full list of genes with statistical metrics in the 29 tumor types is provided in Additional file 1: Table S4 and Additional file 1: Table S5. Each circle represents one gene in each tumor type. For b, genes mutated in at least 5% of the samples in individual tumor types were included in statistical testing, hence shown on the volcano plots. Logistic regression with TMB as a covariate was used in b