Lncap DNA Replication, Recombination and Repair
Supplementary Table 1: LNCaP DNA Replication, Recombination and Repair
Function / MoleculesRepair / ABL1, APEX1, ATM, ATRX, ATXN3, BCL2L1, BRCA1, CDKN2D, CHRNA4, CIB1, CREBBP, DCLRE1C, ERCC4, ERCC8, EXO1, FANCA, FEN1, HGF, HMGB1, HSPA1A, IL1B, KIT, MNAT1, MRE11A, MSH3, NTHL1, OBFC2A, PARP1, PMS2, POLK, RAD1, RAD18, RAD21, RAD54B, RECQL, REV1, RNF168, RPAIN, RRM2B, SIRT1, SOD1, SUMO1, TNF, TRIP13, TYMS, UBE2B, UBE2N, UBE2V
Checkpoint Control / ATM, BUB1, BUB3, BUB1B, CCNB1, CCNG2, CDC7, CDC25C, CHEK2, DBF4, EIF4E, MAD2L1, MAPK14, MCPH1, MRE11A, MYC, NDC80, PMS2, RAD18, TIPIN, ZAK, ZW10
Modification / ABL1, APEX1, ATF2, ATM, ATRX, ATXN3, BCL2L1, BRCA1, CBX1, CBX3, CBX5, CDKN2D, CHRNA4, CIB1, CREBBP, DCLRE1C, ELK1, ERCC4, ERCC8, EXO1, FANCA, FEN1, GATAD2A, HGF, HMGB, HSPA1A, IL1B, KIT, MBD1, MNAT1, MRE11A, MSH3, NCL, NTHL1, OBFC2A, PARP1, PMS2, POLK, RAD1, RAD18, RAD21, RAD54B, RECQL, REV1, RNF168, RPA3, RPAIN, RRM2B, SIRT1, SMARCA5, SOD1, SUB1, SUMO1, TNF, TRIP13, TYMS, UBE2B, UBE2N, UBE2V2, UNG, WRN, XRCC4, XRCC6, XRCC6BP1
Fragmentation / FAS, MAPK9, PTK2, SOD1, TNF
Recombination / ATM, ATRX, BRCA1, DCLRE1C, EXO1, GDNF, HMGB1, HMGN2, KPNA2, MCPH1, MRE11A, MSH3, PSMC3IP, RAD18, RAD21, RAD54B, RECQL, RPAIN, TRIP13, WRN, XRCC4
DSB Repair / ATM, BRCA1, CIB1, DCLRE1C, ERCC4, FEN1, KPNA2, MRE11A, NPM1, OBFC2A, PARP1, RAD21, RNF168, SOD1, TRIP13, UBE2N, XRCC4, XRCC6, XRCC6BP1
Segregation / ATRX, BRCA1, BUB3, CCNA2, CCNB1, CDC14A, ECT2, HDAC4, MAD2L1, NCAPG2, NDC80, NUDCD3, PSEN1, RAN, SKA2, SKA3, SMC2, SRPK1, ZW10
Formation / HDAC7, PML, TNF
Remodeling / BAZ1A, ERCC8, SMARCA5, SOCS6, TNF
Integration / PARP1, SMARCB1, TNPO3, XRCC6
Supplementary Table 2: PCSC1 DNA Replication, Recombination and Repair
Function / MoleculesRepair / APEX1, ASF1A, ATXN3, BCAS2, BCL2L1, BCR, BRCA1, BRCC3, BTG2, CCNO, DCLRE1A, DCLRE1C, DDB2, DEK, DNA2, ERCC1, EXO1, EYA3, FAM175A, FANCA, FEN1, IFNG, MDM2, MSH2, MSH6, NBN, OBFC2A, OGG1, PARP1, PLRG1, POLD1, POLH, POLQ, PRMT6, RAD1, RAD17, RAD50, RAD51C, RAD54B, RARA, RECQL, REV1, RNF168, RPAIN, SETMAR, SETX, SMC1A, TCEA1, TDG, TDP1, TOP1, TP53BP1, TRIP13, UBE2B, UBE2V1, USP1, UVRAG, WRN, XAB2, XRCC4, XRCC6, XRCC6BP1
Modification / ALKBH2, APC, APEX1, ASF1A, ATF7IP, ATXN3, BAZ2A, BCAS2, BCL2L1, BCR, BRCA1, BRCC3, BTG2, CBX1, CCNO, CDK7, CTCF, DCLRE1A, DCLRE1C, DDB2, DEK, DNA2, ELK1, ERCC1, EXO1, EYA3, FAM175A, FANCA, FEN1, FTH1, GATA1, IFNG, MBD1, MCM7, MDM2, MECP2, MSH2, MSH6, NBN, NCL, OBFC2A, OGG1, PARP1, PLRG1, POLD1, POLH, POLQ, PRMT6, RAD1, RAD17, RAD50, RAD51C, RAD54B, RARA, RB1, RECQL, REV1, RNF168, RPA3, RPAIN, SETMAR, SETX, SMC1A, TCEA1, TDG, TDP1, TOP1, TP53BP1, TRIP13, UBE2B, UBE2V1, USP1, UVRAG, WRN, XAB2, XRCC4, XRCC6, XRCC6BP1
Checkpoint Control / BUB3, CCNB1, CDC7, CDC25A, CHEK2, CHFR, DBF4, E2F2, EIF4E, KNTC1, MAD2L1, MCM7, MCPH1, MDM2, MSH2, MXD1, MYC, NBN, POLH, RAD17, RAD50, RB1, SMC1A, TIPIN, TP53BP1, ZWILCH, ZWINT
Replication / AKAP8L, AP1AR, APC, BRCA1, CCDC88A, CCNA2, CDC7, CDC25A, CDKN1B, DBF4, DNA2, E2F2, E4F1, EP300, ERCC1, FAM135A, FEN1, FHIT, GINS1, GMNN, GTPBP4, HELB, HMGA2, HMGN2, HRAS, IL6, ING4, KIN, MAPK8, MCM7, MED1, MYC, NBN, NCL, NR1I3, NUP98, ORC6L, PARP1, PCM1, POLD1, POLD4, POLE3, POLH, PRIM1, PRIM2, RAD17, RB1, REV1, RFC1, RPA3, RPAIN, SIN3A, SOCS3, SPATA7, TBRG1, TFAM, TIMELESS, TIPIN, TMPO, TOP1, TSPYL2, UBA5, VPRBP, WRN
Damage / BDKRB1, BECN1, BIRC5, BRCA1, BRIP1, CASP3, CENPE, CTSS, E2F2, EIF2AK2, EP300, ERCC1, FANCA, GMNN, GSTP1, IFNG, MDM2, MSH2, MYC, NBN, NQO1, OGG1, PARP1, PBK, POLH, PRKCZ, PRNP, RAD51C, RARA, RB1, RECQL, RRM2, RUNX1T1, SETD8, SMG1, TDP1, TOP1, TYR, YWHAE
DSB Repair / BRCA1, BRCC3, CEBPA, DCLRE1C, ERCC1, EYA3, FAM175A, FEN1, IL24, KPNA2, MDM2, MSH2, NBN, OBFC2A, PARP1, RAD50, RNF168, SETMAR, SETX, TDP1, TRIP13, XRCC4, XRCC6, XRCC6BP1
Metabolism / ABCB1, AGAP2, AGTR1, AKAP8L, ANTXR1, AP1AR, APC, APEX1, BARD1, BAX, BCL2L1, BCR, BIRC5, BRCA1, BSG, CASP2, CASP3, CCDC88A, CCNA2, CDC7, CDC25A, CDKN1B, CYCS, DBF4, DDIT3, DNA2, DNASE1L1, E2F2, E4F1, EIF2AK2, EP300, ERCC1, EXO1, FAM135A, FEN1, FFAR3, FHIT, GINS1, GMNN, GTPBP4, GZMM, HELB, HMGA2, HMGN2, HNRNPA1, HRAS, IFNG, IL6, ING4, KIN, KPNA2, MAPK8, MCL1, MCM7, MED1, MYC, NBN, NCL, NR1I3, NUP98, ORC6L, PARP1, PCM1, PIK3CA, POLD1, POLD4, POLE3, POLH, PPIA, PRIM1, PRIM2, PRNP, RAD17, RAN, RB1, REV1, RFC1, RPA3, RPAIN, SIN3A, SOCS3, SPATA7, TBRG1, TFAM, TIAL1, TIMELESS, TIPIN, TMPO, TNFSF10, TOP1, TSPYL2, UBA5, UBQLN1, VPRBP, VPS28, WRN, XRCC6, ZMAT3
S phase Checkpoint Control / CDC25A, DBF4, EIF4E, MCM7, POLH, RAD17, TIPIN, TP53BP1
Segregation / APC, BRCA1, BUB3, CCNA2, CCNB1, DDX11, DSN1, ECT2, GPSM2, HCFC1, MAD2L1, NCAPH2, NDEL1, PSEN1, PSEN2, RAN, RIOK3, SKA1, SKA2, SMC2, SMC4, TAP2, ZWINT
Recombination / BRCA1, DCLRE1C, ERCC1, EXO1, GDNF, HMGA2, HMGN2, KPNA1, KPNA2, MCPH1, MSH2, MSH6, NBN, PSMC3IP, RAD50, RAD51AP1, RAD51C, RAD54B, RECQL, RPAIN, TRIP13, TSN, WRN, XRCC4
DNA Damage Response / APC, BAX, BRCA1, BTG2, CASP3, CDKN1B, CHEK2, DDIT3, DNAJA1, DYRK2, ERCC1, HIPK2, HMOX1, ING4, MAPK1, MCM7, MSH2, MSH6, NBN, NUPR1, PARP1, PLRG1, PMAIP1, PSEN1, RAD1, RAD17, RAD54B, SESN1, SMC1A, SP100, TOP1, UBE2B, WRN, XRCC6
Joining / BRCA1, ETV6, GSTP1, JAK2, NBN, PARP1, PRKCZ, RAD50, TOP1, XRCC4, XRCC6
Breakage / BRIP1, FANCA, MDM2, MYC, NBN, POLH, RAD51C, RECQL
Transcription / HELB, PRIM1, PRIM2
Excision Repair / APEX1, ATXN3, CCNO, DCLRE1A, DDB2, DNA2, ERCC1, EXO1, FEN1, MSH2, MSH6, OGG1, PARP1, POLD1, PRMT6, RARA, TCEA1, TDG, WRN, XAB2
DNA Damage Checkpoint / CCND1, CEBPA, CHEK2, GMNN, NBN, PTPN11, RAD1, RAD17, TIPIN, TP53BP1
Condensation / CDCA5, CDK1, CENPC1, CHFR, CHMP1A, MAD2L1, PAM, ROCK2, SMC2, SMC4
Degradation / IL6, MAPK8, PRNP, PTK2, STAT1
Formation / BAZ1A, BRCA1, CHRAC1, DR1, HDAC8, POLE3, POLE4, SMARCA4, SUV39H2
Supplementary Table 3: PCSC2 DNA Replication, Recombination and Repair
Function / MoleculesRepair / ABL1, ALKBH1, APBB1, APTX, BRCA1, CREBBP, DCLRE1C, DEK, ERBB2, ERCC4, EYA3, FAM175A, FANCA, HMGA1, HMGB1, NBN, NEIL1, OBFC2A, OGG1, PARP2, POLH, PRMT6, RAD1, RAD50, RAD51, RAD23B, RAD54B, RAD9A, REV1, RPAIN, SETMAR, SIRT1, TCEA1, TERT, TGFB1, TNF, TYMS, UBE2B, UBE2V1, UNG, USP1, XRCC4, XRCC6, XRCC3, XRCC6BP1
Modification / ABL1, ALKBH1, APBB1, APTX, BRCA1, CBX1, CREBBP, DCLRE1C, DEK, DHX36, ERBB2, ERCC4, EYA3, FAM175A, FANCA, FTH1, GATAD2A, HELLS, HMGA1, HMGB1, IGF2R, MBD1, MCM4, NBN, NCL, NEIL1, OBFC2A, OGG1, PARP2, POLH, PRMT6, PRMT7, RAD1, RAD50, RAD51, RAD23B, RAD54B, RAD9A, REV1, RPAIN, SETMAR, SIRT1, SMARCA5, TCEA1, TERT, TGFB1, TNF, TRDMT1, TYMS, UBE2B, UBE2V1, UNG, USP1, XRCC4, XRCC6, XRCC3, XRCC6BP1
Metabolism / ABCB1, ABL1, ADIPOQ, AREG, ASAH1, BAX, BIRC5, BRCA1, CASP2, CCDC88A, CCNA2, CDC25A, CDT1, CRYAB, DAPK1, DBF4, DHX9, DUT, GMNN, GZMM, HMGA1, HMGB1, HMGN2, INS, IRF2, MCL1, MED1, MYC, NASP, NBN, NCL, NPM1, NR1I3, NRG1, ORC1L, ORC4L, ORC5L, PDGFA, PDGFB, PML, POLH, POLM, PPIA, PRIM1, PRNP, PTGS2, PTHLH, RAD51, RAN, REPIN1, REV1, RFC1, RPAIN, SIRT1, SRC, SRGN, STK24, TERF2, TFAM, TFF3, TGFB1, THOC1, TIPIN, TMPO, TNF, TNFSF10, TSG101, UBA5, VPRBP, XRCC6
Joining / ABL1, APTX, BRCA1, ETV6, FUS, NBN, RAD50, RAD51, XRCC4, XRCC6
Recombination / BRCA1, DCLRE1C, EME1, EWSR1, GDNF, HMGA1, HMGB1, HMGN2, NBN, PSMC3IP, RAD50, RAD51, RAD51L3, RAD54B, RPAIN, SYCP1, TSN, XRCC4, XRCC3
DSB Repair / APBB1, BRCA1, CEBPA, DCLRE1C, ERCC4, EYA3, FAM175A, NBN, NPM1, OBFC2A, RAD50, RAD9A, SETMAR, TERF2, XRCC4, XRCC6, XRCC6BP1
S phase Checkpoint Control / CDC25A, DBF4, EIF4E, FANCD2, POLH, TIPIN
Replication / AREG, BRCA1, CCDC88A, CCNA2, CDC25A, CDT1, DBF4, DUT, GMNN, HMGA1, HMGB1, HMGN2, INS, MED1, MYC, NASP, NBN, NCL, NPM1, NR1I3, ORC1L, ORC4L, ORC5L, PDGFA, PDGFB, POLH, POLM, PRIM1, PTGS2, REPIN1, REV1, RFC1, RPAIN, SIRT1, TFAM, TGFB1, TIPIN, TMPO, TSG101, UBA5, VPRBP
DNA Damage Response / ABL1, APBB1, APTX, BAX, BAZ1B, BCL3, BRCA1, CHEK2, DNAJA1, FANCD2, NBN, PMAIP1, PML, RAD1, RAD51, RAD23B, RAD54B, RAD9A, SESN1, SIRT1, SP100, TP73, UBE2B, XRCC6, XRCC3
Remodeling / BAZ1A, MST1R, SMARCA5, TNF, TTF1
Damage / BRCA1, FANCA, MYC, NBN, PARP2, POLH, RTEL1, TERT
Stabilization / C9ORF80, DCLRE1C, HNRNPAB, MYC, NBN, PARP2, RAD51L3, RAN, TERT, XRCC6
Formation / BAZ1A, BAZ1B, BRCA1, CHRAC1, MYC, POLE4, SMARCA5, SYCP1, TERF2, TLK1, TSG101
Segregation / ARL8B, BRCA1, BUB3, CCNA2, DDX11, ECT2, EIF3E, GPSM2, NCAPG2, PPP2R5A, RAN, RIOK3, SKA1, SMC4, TAP2, ZWINT
Checkpoint Control / BUB3, CCNG2, CDC25A, CHEK2, DBF4, EIF4E, FANCD2, MXD1, MYC, NBN, POLH, RAD50, RAD9A, TIPIN, ZWINT
Elongation / ACD, NBN, POT1, RTEL1, TERT
Instability / BECN1, DYNLL1, EME1, KRAS, MYC, RASSF1, SHPRH, TERT, TNF, TXN
Re-replication / CCDC88A, CCNA2, CDT1, GMNN, NBN
Homologous Recombination / BRCA1, EWSR1, FANCD2, GDNF, NBN, PSMC3IP, RAD50, RAD51, RAD51L3, RAD54B, SYCP1, XRCC3
DNA Damage Checkpoint / CEBPA, CHEK2, GMNN, NBN, PTPN11, RAD1, RAD9A, TIPIN
Breakage / FANCA, MYC, NBN, PARP2, POLH, RTEL1
DNA Replication Checkpoint / CDT1, CENPE, RAD9A, TIPIN
Alignment / BIRC5, CAPN2, CCNA2, CENPE, HOXA7, NCAPG2, SMC4
Cleavage / EME1, FTH1, HMGB1, MYC, NBN, NEIL1, OGG1, RAD50, TNF, UNG
Assembly / BAZ1A, BAZ1B, CBXX1, CHRAC1, POLE4, RAN, SMARCA5, TLK1
Homologous Recombination Repair / BRCA1, ERCC4, RAD51, RAD54B, XRCC4, XRCC6
Acetylation / ADA, TP73
Conversion / DHX36, FTH1
Annealing / ABL1, ETV6, FUS
Fragmentation / ABCB1, ABL1, PTHLH
Supplementary Table 4: PCSC3 DNA Replication, Recombination and Repair
Function / MoleculesReplication / AP1AR, CCDC88A ,CCNA2, CDC6, CDC7, CDC25A, CDC45L, DB4, DUT, ENDOG, EP300, FEN1, GMNN, GTPBP4, HBEGF, HMGB1, HMGN1, HMGN2, ID3, IGF1R, ING4, KIAA0101, KIN, MCM3, MCM3AP, MYC, NAE1, NBN, NCL, NPM1, NR1I3, ORC2L, ORC4L, ORC5L, ORC6L,
PCM1, PCNA, PDGFB, PDGFRA, POLA1, POLA2, POLH PRIM1, PRIM2, PTGS2, RB1, RECQL5, RFC1, RNASEH2A, RPA3, SMARCB1, SOCS3, TFAM, TGFB1, TIMELESS, TIPIN, TP53, TSPYL1, WRN, XRCC5
Checkpoint Control / CCNB1, CCNG2, CDC6, CDC7, CDC25A, CDK10, DBF4, EIF4E, MAD2L1, MCPH1, MDC1, MDM2, MYC, NBN, NDC80, PIN1, POLH, RAD50, RAE1, RB1, TIPIN, TP53, XPC, ZWILCH, ZWINT
Metabolism / ABL1, ADRA1D, AIFM1, ANGPT1, AP1AR, APEX1, BAX, C5, CCDC88A, CCNA2, CD47, CDC6, CDC7, CDC25A, CDC45L, DBF4, DHX9, DUT, ENDOG, EP300, EXO1, FEN1, GMNN, GTPBP4, HBEGF, HMGB1, HMGN1, HMGN2, HSD17B10, ID3, IGF1R, ING4, INHBA, ITGB3, KIAA0101, KIN, KPNA2, MCL1, MCM3, MCM3AP, MYC, NAE1, NBN, NCL, NPM1, NR1I3, NR3C1, NRAS, NRG1, NT5E, ORC2L, ORC4L, ORC5L, ORC6L, PCM1, PCNA, PDGFB, PDGFRA, PIK3CA, POLA1, POLA2, POLH, PPP1CC, PPT1, PRIM1, PRIM2, PRNP, PTGS2, RAD51, RAN, RB1, RECQL5, RFC1, RNASEH2A, RPA3, SMARCB1, SNCA, SOCS3, SOD1, TFAM, TGFB1, TIA1, TIMELESS, TIPIN, TP53, TSPYL1, UBQLN1, WRN, XRCC5, XRCC6
Recombination / ATRX, DCLRE1C, EWSR1, EXO1, HMGB1, HMGN1, HMGN2, KPNA2, LIG3, MCPH1, MLH1, NBN, PSMC3IP, RAD21, RAD50, RAD51, RAD51C, RAD54B, REC8, RECQL, TP53, TSN, WRN, XRCC5
DSB Repair / BRCC3, CEBPA, DCLRE1C, FEN1, KPNA2, MDM2, MLH1, NBN, NHEJ1, NPM1, OBFC2A, PCNA, POLA1, RAD21, RAD50, SETMAR, SMAD3, SOD1, TP53, XRCC5, XRCC6
Repair / ABL1, APEX1, ATRX, BRCC3, CCNO, CDC5L, CREBBP, DCLRE1C, DEK, ERBB2, EXO1, FANCA, FEN1, HINFP, HMGB1, HMGN1, ING1, LIG3, MDM2, MLH1, MNAT1, MUTYH, NBN, NHEJ1, OBFC2A, PCNA, POLA1, POLH, POLK, RAD21, RAD50, RAD51, RAD51C, RAD54B, RECQL, RECQL5, SETMAR, SMUG1, SOD1, TDG, TGFB1, TP53, TYMS, UBE2V1, USP1, WRN, XPC, XRCC5, XRCC6
Modification / ABL1, APEX1, ATRX, BRCC3, C10ORF2, CBX3, CCNO, CDC5L, CREBBP, DCLRE1C, DEK, DMAP1, ERBB2, EXO1, FANCA, FEN1, FTH1, HINFP, HMGB1, HMGN1, IGF2R, ING1, LIG3, MDM2, MLH1, MLL, MNAT1, MUTYH, MYB, NBN, NCL, NHEJ1, OBFC2A, PCNA, PIWIL2, POLA1, POLH, POLK, PRMT7, RAD21, RAD50, RAD51, RAD51C, RAD54B, RB1, RECQL, RECQL5, RPA3, SETMAR, SMUG1, SNCA, SOD1, SRF, TDG, TGFB1, TP53, TYMS, UBE2V1, USP1, WRN, XPC, XRCC5, XRCC6
Segregation / ATRX, CCNA2, CCNB1, CCNB2, CDC42, ECT2, EIF3E, ESPL1, HCFC1, MAD2L1, MLH1, NCAPH2, NDC80, NEK9, PSEN2, RAN, SKA2, SKA3, SMC4, TAP2, ZWINT
Breakage / FANCA, MDM2, MYC, NBN, POLH, RAD51C, RECQL, SOD1
Re-replication / CCDC88A, CCNA2, CDC6, GMNN, NBN, TP53
Chromosomal Congression / CENPE, KIF22, KIF18A, MAD2L1, NDC80
Homologous Recombination / EWSR1, LIG3, MCPH1, MLH1, NBN, PSMC3IP, RAD21, RAD50, RAD51, RAD51C, RAD54B, REC8, TP53, WRN
Mismatch Repair / ABL1, EXO1, HMGB1, MLH1, MUTYH, PCNA, TP73, XRCC5
Damage / AIFM1, BECN1, CENPE, DICER1, EP300, FANCA, LRP1, MCM10, MDM2, MYC, NBN, PAXIP1, PBK, PLK1, PROX1, PRNP, POLH, RAD51C, RB1, RECQL, RRM2, SETD8, SMG1, SOD1, TP53, XRCC5, YWHAE
Alignment / CAPN2, CCNA2, CENPE, HCFC1, KIF22, KIF18A, PLK1, SMC4
Formation / CKAP2, EIF3E, FBXO5, KIF11, KIF2A, MND1, MDM2, NEK9, PCNA, PLK1, PSMC3IP, RAE1, RAN, RCC1, TP53, TUBG1
S phase Checkpoint Control / CDC25A, DBF4, TIPIN
Stabilization / HNRNPAB, MYC, NBN