Table 1.
DNA repair genes and their associated DNA repair-related pathways investigated in this study.
| Acronym | DNA Repair Pathways | No. of Genes 1 | Gene Name (UniProtKB accession ID) |
|---|---|---|---|
| Major DNA Repair Pathways | |||
| BER | Base excision repair | 38 | APEX1 (P27695); CCNO (P22674); ERCC1 (P07992); ERCC4 (Q92889); ERCC5 (P28715); ERCC6 (Q03468); FEN1 (P39748); GADD45A (P24522); HUS1 (O60921); LIG1 (P18858); LIG3 (P49916); MBD4 (O95243); MPG (P29372); MUTYH (Q9UIF7); NEIL1 (Q96FI4); NEIL2 (Q969S2); NEIL3 (Q8TAT5); NTHL1 (P78549); OGG1 (O15527); PARP1 (P09874); PARP2 (Q9UGN5); PARP3 (Q9Y6F1); PCNA (P12004); POLB (P06746); POLD3 (Q15054); RAD23A (P54725); RAD23B (P54727); RAD52 (P43351); RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); SIRT1 (Q96EB6); SMUG1 (Q53HV7); TDG (Q13569); TP53 (P04637); UNG (P13051); WRN (Q14191); XRCC1 (P18887) |
| NER | Nucleotide excision repair | 37 | ATR (Q13535); ATXN3 (P54252); CCNH (P51946); CDK7 (P50613); CETN2 (P41208); DDB1 (Q16531); DDB2 (Q92466); ERCC1 (P07992); ERCC2 (P18074); ERCC3 (P19447); ERCC4 (Q92889); ERCC5 (P28715); ERCC6 (Q03468); ERCC8 (Q13216); GADD45A (P24522); GTF2H1 (P32780); GTF2H2 (Q13888); GTF2H3 (Q13889); GTF2H4 (Q92759); LIG1 (P18858); LIG3 (P49916); MMS19 (Q96T76); NTHL1 (P78549); OGG1 (O15527); PCNA (P12004); POLD3 (Q15054); RAD23A (P54725); RAD23B (P54727); RFC1 (P35251); RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); SIRT1 (Q96EB6); TP53 (P04637); XAB2 (Q9HCS7); XPA (P23025); XRCC1 (P18887) |
| MMR | Mismatch repair | 19 | ABL1 (P00519); EXO1 (Q9UQ84); MLH1 (P40692); MLH3 (Q9UHC1); MSH2 (P43246); MSH3 (P20585); MSH4 (O15457); MSH5 (O43196); MSH6 (P52701); PCNA (P12004); PMS1 (P54277); PMS2 (P54278); POLD3 (Q15054); RFC1 (P35251); RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); TDG (Q13569); TREX1 (Q9NSU2) |
| HRR | Homologous recombinational repair | 49 | ATM (Q13315); ATR (Q13535); BLM (P54132); BRCA1 (P38398); BRCA2 (P51587); BRIP1 (Q9BX63); CHEK1 (O14757); DMC1 (Q14565); ERCC1 (P07992); ERCC4 (Q92889); ERCC6 (Q03468); FANCA (O15360); FANCB (Q8NB91); FANCF (Q9NPI8); FANCG (O15287); FEN1 (P39748); GADD45A (P24522); H2AFX (P16104); HUS1 (O60921); LIG3 (P49916); MDC1 (Q14676); MRE11 (P49959); MSH2 (P43246); MSH4 (O15457); MSH5 (O43196); MSH6 (P52701); NBN (O60934); PARP1 (P09874); PARP2 (Q9UGN5); PARP3 (Q9Y6F1); RAD17 (O75943); RAD21 (O60216); RAD50 (Q92878); RAD51 (Q06609); RAD51B (O15315); RAD51C (O43502); RAD51D (O75771); RAD52 (P43351); RAD54B (Q9Y620); RAD54L (Q92698); REV1 (Q9UBZ9); RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); SIRT1 (Q96EB6); TP53BP1 (Q12888); WRN (Q14191); XRCC1 (P18887); XRCC2 (O43543) |
| NHEJ | Non-homologous end-joining | 22 | ATM (Q13315); ATP23 (Q9Y6H3); BRCA1 (P38398); ERCC1 (P07992); ERCC4 (Q92889); LIG4 (P49917); MDC1 (Q14676); MLH1 (P40692); MRE11 (P49959); NBN (O60934); PARP1 (P09874); PARP2 (Q9UGN5); PARP3 (Q9Y6F1); PRKDC (P78527); RAD50 (Q92878); SIRT1 (Q96EB6); TP53BP1 (Q12888); WRN (Q14191); XRCC1 (P18887); XRCC4 (Q13426); XRCC5 (P13010); XRCC6 (P12956) |
| Other DNA Repair Pathways | |||
| POL | Polymerases | 4 | PCNA (P12004); POLB (P06746); POLD3 (Q15054); REV1 (Q9UBZ9) |
| DRD | Direct reversal of damage | 3 | ALKBH1 (Q13686); ALKBH3 (Q96Q83); MGMT (P16455) |
| SMNP | Sanitization/modulation of nucleotide pools | 3 | DUT (P33316); NUDT1 (P36639); RRM2B (Q7LG56) |
| FA | Fanconi anemia | 9 | BRCA1 (P38398); BRCA2 (P51587); BRIP1 (Q9BX63); FANCA (O15360); FANCB (Q8NB91); FANCF (Q9NPI8); FANCG (O15287); RAD51 (Q06609); RAD51C (O43502) |
| TLM | Telomere maintenance | 26 | ATR (Q13535); BRCA1 (P38398); BRCA2 (P51587); ERCC1 (P07992); ERCC4 (Q92889); FEN1 (P39748); MRE11 (P49959); NBN (O60934); PARP1 (P09874); PARP3 (Q9Y6F1); PCNA (P12004); POLD3 (Q15054); RAD50 (Q92878); RAD51 (Q06609); RAD51C (O43502); RAD51D (O75771); RFC1 (P35251) RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); SIRT1 (Q96EB6); TP53 (P04637); WRN (Q14191); XRCC1 (P18887); XRCC5 (P13010); XRCC6 (P12956) |
| TLS | Translesion synthesis | 3 | PCNA (P12004); POLD3 (Q15054); REV1 (Q9UBZ9) |
| CSM | Chromatin structure and modification | 16 | CHEK1 (O14757); ERCC6 (Q03468); FEN1 (P39748); H2AFX (P16104); LIG3 (P49916); PCNA (P12004); RAD17 (O75943); RAD21 (O60216); RAD51 (Q06609); RAD51C (O43502); RPA1 (P27694); RPA2 (P15927); RPA3 (P35244); SIRT1 (Q96EB6); TP53 (P04637); XRCC1 (P18887) |
| MMEJR | Microhomology-mediated end-joining repair | 6 | FEN1 (P39748); LIG3 (P49916); MRE11 (P49959); NBN (O60934); PARP1 (P09874); XRCC1 (P18887) |
| SDA | Genes defective in diseases associated with sensitivity to DNA-damaging agents | 7 | ATM (Q13315); ATXN3 (P54252); BLM (P54132); ERCC6 (Q03468); ERCC8 (Q13216); NBN (O60934); WRN (Q14191) |
| UBM | Ubiquitination and modification (Rad6 pathways) | 6 | RAD18 (Q9NS91); SHPRH (Q149N8); UBE2A (P49459); UBE2B (P63146); UBE2N (P61088); UBE2V2 (Q15819) |
| OTHER | Other DNA damage-related | 4 | CRY1 (Q16526); SUMO1 (P63165); TOP3A (Q13472); TOP3B (O95985) |
1 These numbers add up to over 117 (the total number of genes studied) because some of the genes are involved in more than one pathway.