Table 4.
Multiple-pathway results showing DNA Repair genes whose upregulation or downregulation prolongs overall survival for subjects with RNA-Seq data in TCGA. Cancers listed had significant empirical p-value test results (p < 0.05). a
| Cancer | Predictors | Upregulation Prolongs OS | Downregulation Prolongs OS |
|---|---|---|---|
| AML * | Genes | POLN | RAD23A, APEX2, EME2 |
| Pathways (%) | TLS (100.0) | DDS (33), BER (33), HRR (33), | |
| Bladder * | Genes | BLM, RAD9A, MGMT, LIG1, MUTYH, DDB1, ERCC5, XPC, FANCD2, MSH5, DCLRE1C, REV1 | FANCC, ALKBH2, APEX2, LIG3, POLB, GTF2H5, PMS1, PRKDC, REV3L |
| Pathways (%) | DDS (16.7), DRR (8.3), BER (16.7), NER (25.0), HRR (16.7), NHEJ (8.3), TLS (8.3) | DDS (11.1), DRR (11.1), BER (33.3), NER (11.1), MMR (11.1), NHEJ (11.1), TLS (11.1) |
|
| Sarcoma * | Genes | MNAT1, APEX1, APTX, FEN1, NEIL3, DDB1, GTF2H3, FANCI, PRKDC | DCLRE1B, POLL, CUL4A, ERCC2, MSH2, FANCG |
| Pathways (%) | DDS (11.1), BER (44.4), NER (22.2), HRR (11.1), NHEJ (11.1) | DDS (16.7), BER (16.7), NER (33.3), MMR (16.7), HRR (16.7) | |
| Breast | Genes | RAD50, PMS1 | ATRIP, FANCC, RAD1, RFC3, NEIL3, EXO1, FANCB, FANCD2, FANCI, RAD51, XRCC4 |
| Pathways (%) | DDS (50.0), MMR (50.0) | DDS (36.4), BER (9.1), MMR (9.1), HRR (36.4), NHEJ (9.1) |
|
| Colorectal | Genes | DCLRE1C | RAD23A, RFC2, POLL, MLH3, FANCL |
| Pathways (%) | NHEJ (100.0) | DDS (40.0), BER (20.0), MMR (20.0), HRR (20.0) |
|
| Renal Papillary | Genes | RAD17, OGG1, DDB2, ERCC2 | BLM, RAD1, FEN1, LIG1, EXO1, MSH6, BRCA2, EME1, FANCB, LIG4 |
| Pathways (%) | DDS (25.0), BER (25.0), NER (50.0) | DDS (20.0), BER (20.0), MMR (20.0), HRR (30.0), NHEJ (10.0) | |
| Lung | Genes | RAD17, ALKBH3, MGMT, MPG, NEIL1, XPC, LIG4, POLK, REV3L | BRCA1, NBN, RAD1, NEIL3, MMS19, FANCI, XRCC5 |
| Pathways (%) | DDS (11.1), DRR (22.2), BER (22.2), NER (11.1), NHEJ (11.1), TLS (22.2) | DDS (42.9), BER (14.3), NER (14.3), HRR (14.3), NHEJ (14.3) | |
| Lung Sq. Cell | Genes | CHEK2, MNAT1, APTX, TDG, FANCE, FANCL | XRCC1 |
| Pathways (%) | DDS (33.3), BER (33.3), HRR (33.3) | BER (100.0) | |
| Melanoma | Genes | ATM, MNAT1, MBD4, NEIL1, ERCC5, RAD23B, DCLRE1C | MDC1, NBN, MUTYH, POLE, UNG, FANCE, FANCI, POLI, POLK |
| Pathways (%) | DDS (28.6), BER (28.6), NER (28.6), NHEJ (14.3) |
DDS (22.2), BER (33.3), HRR (22.2), TLS (22.2) |
|
| Stomach | Genes | CUL4A, POLQ | |
| Pathways (%) | NER (50.0), TLS (50.0) |
a—Liver cancer not included because it was not a parsimonious model (43 repair genes). * Stage not available, expression adjusted only by age and PCNA metagene.