Fig. 3

Immune cell infiltration predicts clinical outcome. a Association of tumor infiltrating immune cells with patient survival. For each cancer type, multivariate Cox regression was performed, with covariates including the abundance of six immune cell types, patient age at diagnosis, clinical stage, and viral infection status when available. Each entry on the first six rows of the heatmap represents the hazard ratio (HR) of a corresponding immune cell type, with larger size indicating statistical significance at a false discovery rate (FDR) of 0.15 and color indicating the value of the HR. The last row of the heatmap records the Cox model HRs and statistical significance using cytolytic activity (CYT) scores adjusted for the same covariates. Multiple test correction was performed using q value across cancer types and six immune components. b Kaplan–Meier curves of melanoma (SKCM) and head and neck cancer (HNSC) stratified by infiltration CD8 T-cell abundance. Median survival time for the top 20 % of patients in melanoma and head and neck cancers is 4507 and 1838 days, respectively, and for bottom 20 % 2005 and 862 days, respectively. Statistical significance, hazard ratios, and 95 % confidence intervals were calculated using multivariate Cox regression and all the samples as described above. c CD8 T-cell infiltration in primary tumors (metastatic samples for SKCM) significantly (FDR ≤ 0.15) predicts tumor relapse in selected cancers. Statistical significance was evaluated using logistic regression correcting for patient age and clinical stage