Statistical analysis

In comparisons of two classes of normally-distributed data, such as gene expression levels, we used the two-tailed Student’s t test. We used the one-tailed Mann- Whitney U test to compare two classes of non-normally distributed data, such as TIL levels in pathological sections, ssGSEA scores, ITH scores, TMB, and HRD scores. Fisher’s exact test was utilized to analyze the association between two categorical variables. To adjust for P-values in multiple tests, FDRs were calculated using the Benjamini-Hochberg method (37). We performed all statistical analyses with the R programming language (version 3.6.1).