Additional file 1 of Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types

Table S1. List of datasets used in this study (TCGA, external cancer genomic databases (ICGC, CPTAC, and MET500), and a cohort of patients treated with anti-PD1 from a published study). Table S2. List of cancer ID and description from TCGA included in this study. Table S3. List of the 160 genes from the T cell-inflamed expression signature. Table S4. List of mutated genes investigated in the individual cancer type analysis that are relatively enriched in non-T cell-inflamed relative to T cell-inflamed tumors. All genes are shown without filtering by p-values. Table S5. List of mutated genes investigated in the individual cancer type analysis that are relatively enriched in T cell-inflamed relative to non-T cell-inflamed tumors. All genes are shown without filtering by p-values. Table S6. List of mutated genes investigated in the pan-cancer analysis that are relatively enriched in non-T cell-inflamed relative to T cell-inflamed tumors. All genes are shown without filtering by p-values. Table S7. List of mutated genes investigated in the pan-cancer analysis that are relatively enriched in T cell-inflamed relative to non-T cell-inflamed tumors. All genes are shown without filtering by p-values. Table S8. Annotation of mutation effects (LOF, GOF, etc.) for NSSMs from genes associated with non-T cell-inflamed phenotype (n = 29, from Fig. 3a) and genes associated with the T cell-inflamed phenotype (n = 3, from Fig. 3b). Table S9. Distribution of tumor samples carrying NSSMs in genes associated with non-T cell-inflamed phenotype (n = 29, from Fig. 3a) or genes associated with the T cell-inflamed phenotype (n = 3, from Fig. 3b) by mutation effect categories (LOF, GOF, etc.). Table S10. List of 266 pathways predicted to be activated in non-T cell-inflamed relative to T cell-inflamed tumors. 1 = activated; 0 = not-activated. Table S11. RPPA validation of activated transcriptional programs at protein level. Table S12. List of genes carrying NSSMs enriched in non-T cell-inflamed tumors (n = 29, from Fig. 3a) or transcriptional programs activated in non-T cell-inflamed tumors across at least 4 cancer types (n = 31, from Fig. 4a) at per patient level. Table S13. Summary of samples carrying NSSMs enriched in non-T cell-inflamed tumors (n = 29, from Fig. 3a) or transcriptional programs activated in non-T cell-inflamed tumors (n = 266). Table S14. Heterogeneity analysis of the NSSM and pathway score distribution across different tumor types. Table S15. Linear regression model of the T cell-inflamed gene expression and NSSM or pathway scores. Table S16. List of drugs targeting relevant molecular mechanisms identified in our study from The Drug Gene Interaction Database (DGIdb). Table S17. Three-level literature review of the genes associated with the non-T cell-inflamed phenotype (n = 29, from Fig. 3a) and genes associated with the T cell-inflamed phenotype (n = 3, from Fig. 3b). (XLSX 22 mb)