Extended Data Fig. 4: Correlation of DeepNeo predictions with TCR scores in TCGA samples.

a, Comparison of the TCR (T cell receptor) signature score between groups of high- and low- immunogenic neoantigen load as predicted by DeepNeo-MHC I and -MHC II. The difference between the two groups is calculated by the two-sided Welch t test. The boxplot’s box represents 25th and 75th percentile with center bar as median value and whiskers represent furthest outlier ≤1.5× the interquartile range from the box. b-c, Correlation of the TCR signature score with b, immunogenic neoantigen load and c, TMB across TCGA cancer types. For the TMB analyses, we used matching TCGA samples with available MHC I or II genotypes. The size and color of dots represent the number of samples per cancer type used in the analysis. The shaded area represents 95 percent confidence interval for fitted line.