Identification of T cell–inflamed and non-T cell–inflamed groups

The tumor groups were identified by our previously published method (13). In brief, unsupervised hierarchical clustering was used to cluster 18,475 genes that are expressed in at least 50% of the samples into 12 groups based on similar expression patterns. A cluster of 1,015 genes including 12 genes of a previously identified T-cell gene signature (CD8A, CCL3, CCL4, CXCL9, CXCL10, ICOS, IRF1, GZMK, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB) was selected for identification of T cell–inflamed, intermediate and non-T cell–inflamed tumor groups using a consensus sample clustering method. Gene ontology (GO) enrichment analysis of the genes of interest was performed using DAVID v6.7 (16).