In particular, we observed that RB1 mutations correlated with E2F family gene upregulations (for example, E2F1; Supplementary Data 7; Supplementary Fig. 20) in bladder urothelial carcinoma (BLCA), BRCA, glioblastoma multiforme (GBM), lung squamous cell carcinoma (LUSC), ovarian serous cystadenocarcinoma (OV) and uterine corpus endometrioid carcinoma (UCEC; Table 1), as well as genes encoding mini-chromosome maintenance proteins, for example, MCM5 (Supplementary Data 7; Supplementary Fig. 21) in BRCA, GBM, lung adenocarcinoma, LUSC and OV. Here, RB1 is linked to bladder transitional cell carcinoma.