168, HIST1H4E, BAZ1B, HIST1H4D, CSN3, MSH2, ASCC

168, HIST1H4E, BAZ1B, HIST1H4D, CSN3, MSH2, ASCC2, FAM175A, HAP1, POLE2, INO80C, MED1, INO80B, EYA3, EYA2, NEIL2, ZBTB32, FANCI, PMS2, MBD4. GTF2H4, POLM, COPS3, USP10, HIST1H2BI, POLL, APITD1, POLE, PIAS4, XPC, KIAA1530, XPA, UBC, HERC2, ATRIP, POLR2J, TFPT, NFRKB, LIG3, CUL4A, AM152 biological activity ALKBH3, GPS1, ERCC6, RAD51L3, C1orf86, ERCC2, KDM4B, HIST1H4L, ABL1, RTEL1, PNKP, HIST3H3, C19orf40, UBE2N, DDB2, BACH1, CDS1, SUMO3, DCLRE1A, NTHL1, HIST2H4B, RAD50, WHSC1. VIPR2, PRKCH, VIPR1, GPR39, F2R, OXT, GNAL, HRH3, TACR2, NRG1, GOLT1A, MCHR1, CRH, TAS1R2, DUSP1, BICD1, NPSR1, CCKAR, PDE4D, PDE4B, RAMP1, PSMD11, RGS4, CSK, RGS7, RHOG, DLG1, OR2C3, DUSP10, GPR4, GPR120, ADRB1, GRM2, CX3CR1, GCGR, OR1F2P, UTS2R, CCBP2, EDN2, JAK3, GPR109A, EDNRB, PTGER1, RASGRF2, TAS2R39, JAK3, OR52W1, IL3RA, OPRK1, ADRB1, ADRB3, CXCR4, BDKRB1, KALRN, CXCR7, GPR84, VAV3, KSR1, FPR3, VAV1, OR51B2, OR52H1, CXCL9, OR8S1, AVP, CXCL5, PSMB5, OR10A3, ABHD6, G6PC, CALCR, PROKR2, GPR84, TIAM1, HTR1D, OR52I1, GALR3, FGF22, CCL22, DHH, RASGRP1, MMP2, GPR68, HBEGF, OR6B3, C5, PIK3R5, CREM, GRM6, GRM8, OR52B6, CCR7, GRPR, AKT1, RASGRF1, CCR9, RASGRF2, SRC, C5AR1, FGFR1, PSMD1, IL8, F2, RASA4, GNRH2, MCHR1, PVR, GNG4, EMR2, GNG8, CCL19, TAAR8, PSMC5, GNA11, GPR4, RAC1, GNAT3, GNA13, RGS10, GRIN1, PRKCQ, RGS13, NET1, OR2A25, PSAP.DGKZ, DLG4, CNKSR1, DGKQ, PRKCA, ABR, RPS6KA2, DGKI, PTCH2, SHH, PTCH2, DGKD, RGR, OR1L3, LTB4R, SPTBN5, SPTBN4, GNG12, TAS1R1, OR4F6, OR4F5, CSF2, OR4F4, PDE4C, RASGEF1A, RHO, RGS9, GHR, ADM2, PRKAR2B, GRM5, IL17RD, MC5R, PPP1CA, SOS2, CCL17, TIAM2, FGD4, TBXA2R, NPFFR1, HRH1, TRPM2, IL17RD, GRK5, CXCR5, PDE2A, ABR, OR10V1, PDGFRB, PDGFRA, MS-275 site OR2B11, FGD3, OR2A7, FGD4, PROKR1, GLP2R, PLCB2, CD97, KL, SHC2, AGT, WNT9A, ARHGEF16, OR2A4, ARHGEF17, OR51I2, OR2A1, EGFR, AGT, ARHGEF7, HCRTR1, KISS1R, PIK3R1, PIK3R2, PDPK1, MAP2K2, OR6B1, OR6B2, OR9Q2, CX3CL1, PTAFR, ARHGEF4, ARHGEF3, PDGFA, CCL28, OR2A42, CCL27, PLEKHG5, FGF3, FGF4, GAB2, ITPR1, F2RL3, ITPR3, LPAR1, PIK3CG, ADCY7, RASAL2, PPYR1, WNT1, ADCY9, MC1R, CCL17, KLB, GALR2, PNOC, GPR176, FFAR1, FFAR2, S1PR5, DAGLA, CSF2RA, NPBWR2, NPBWR1, GRIN2D, TRPC7, ADRBK1, TAS1R3, SSTR4, GHRL, ADORA3, SSTR2, SSTR3, NRG2, RLN3. HIST1H3F, BRD1, HDAC3, HIST1H2BG, SMARCA4, HIST1H2BK, KDM5B, MLL2, EZH2, MLL4, ACTL6B, DNMT3A, MTA3, HCFC1, EATS4, YEATS2, PRMT5, KDM4A, MORF4L2, HIST1H4E, ARID1B, HIST1H4D, TADA2B, C12orf41, HIST1H2AL. DR1, HIST1H2BI, CHD3, KDM3B, CHD4, MLL, TRRAP, HIST1H3D, KDM5C, SAP130, HIST1H3E, PADI2, PADI6, MTA1, PRDM16, PADI1, TRRAP, KIAA1267, NSD1, KDM4B, HIST1H4L, SMARCD3, EP400, RUVBL2, SUPT3H, DOT1L,SUZ12P, KAT2A, FAM48A, HIST2H4B, WHSC1, GATAD2A, KDM5C, SUV39H2, ASH2L, HIST3H3, NCOR2, HDAC10, JAK2, EHMT1, CSRP2BP, KDM6B, PRMT7, CREBBP, KDM6B, HIST3H3, SETD3, RBP1, SETD1B, SETD7, ING5, SMYD2, MBD3, AEBP2, KDM2B, WDR5. (Continued)Immune SystemDNA RepairSignaling by GPCRChromatin organizationPLOS ONE | DOI:10.1371/journal.pone.0157866 June 29,10 /Methylation Landscape of Breast Cancer Cells in Response to ResveratrolTable 2. (Continued) Pathway name Cellular responsesto stress Number of genes 106 Hypermethylated (bold letters) and hypomethylated genes MAPKAPK5, MTMR14, UBE2D1, HIST1H2BG, HSPA2, NUP133, HIST1H2BK, CCS, EZH2, HBXIP, IL8, NUP98, TNIK, GPX7, CABIN1, FZR1, MTOR, ASF1A, HIST1H4E, MAP2K3, HIST1H4D, WDR45L, MAPK10, CBX6, POM121C, MINK1, NECAB3, SCMH1, HSPA12A, EPAS1, HIST1H2AL. HSPA6, HSPA7, HSPA4L, GPX2, HSPA13, GPX1, WIPI2, HIST1H2BI, PC, BAG5, HIST1H3D, MAP1LC3B, HSPA8, HIST1H3E, MAP1LC3A, CDKN.168, HIST1H4E, BAZ1B, HIST1H4D, CSN3, MSH2, ASCC2, FAM175A, HAP1, POLE2, INO80C, MED1, INO80B, EYA3, EYA2, NEIL2, ZBTB32, FANCI, PMS2, MBD4. GTF2H4, POLM, COPS3, USP10, HIST1H2BI, POLL, APITD1, POLE, PIAS4, XPC, KIAA1530, XPA, UBC, HERC2, ATRIP, POLR2J, TFPT, NFRKB, LIG3, CUL4A, ALKBH3, GPS1, ERCC6, RAD51L3, C1orf86, ERCC2, KDM4B, HIST1H4L, ABL1, RTEL1, PNKP, HIST3H3, C19orf40, UBE2N, DDB2, BACH1, CDS1, SUMO3, DCLRE1A, NTHL1, HIST2H4B, RAD50, WHSC1. VIPR2, PRKCH, VIPR1, GPR39, F2R, OXT, GNAL, HRH3, TACR2, NRG1, GOLT1A, MCHR1, CRH, TAS1R2, DUSP1, BICD1, NPSR1, CCKAR, PDE4D, PDE4B, RAMP1, PSMD11, RGS4, CSK, RGS7, RHOG, DLG1, OR2C3, DUSP10, GPR4, GPR120, ADRB1, GRM2, CX3CR1, GCGR, OR1F2P, UTS2R, CCBP2, EDN2, JAK3, GPR109A, EDNRB, PTGER1, RASGRF2, TAS2R39, JAK3, OR52W1, IL3RA, OPRK1, ADRB1, ADRB3, CXCR4, BDKRB1, KALRN, CXCR7, GPR84, VAV3, KSR1, FPR3, VAV1, OR51B2, OR52H1, CXCL9, OR8S1, AVP, CXCL5, PSMB5, OR10A3, ABHD6, G6PC, CALCR, PROKR2, GPR84, TIAM1, HTR1D, OR52I1, GALR3, FGF22, CCL22, DHH, RASGRP1, MMP2, GPR68, HBEGF, OR6B3, C5, PIK3R5, CREM, GRM6, GRM8, OR52B6, CCR7, GRPR, AKT1, RASGRF1, CCR9, RASGRF2, SRC, C5AR1, FGFR1, PSMD1, IL8, F2, RASA4, GNRH2, MCHR1, PVR, GNG4, EMR2, GNG8, CCL19, TAAR8, PSMC5, GNA11, GPR4, RAC1, GNAT3, GNA13, RGS10, GRIN1, PRKCQ, RGS13, NET1, OR2A25, PSAP.DGKZ, DLG4, CNKSR1, DGKQ, PRKCA, ABR, RPS6KA2, DGKI, PTCH2, SHH, PTCH2, DGKD, RGR, OR1L3, LTB4R, SPTBN5, SPTBN4, GNG12, TAS1R1, OR4F6, OR4F5, CSF2, OR4F4, PDE4C, RASGEF1A, RHO, RGS9, GHR, ADM2, PRKAR2B, GRM5, IL17RD, MC5R, PPP1CA, SOS2, CCL17, TIAM2, FGD4, TBXA2R, NPFFR1, HRH1, TRPM2, IL17RD, GRK5, CXCR5, PDE2A, ABR, OR10V1, PDGFRB, PDGFRA, OR2B11, FGD3, OR2A7, FGD4, PROKR1, GLP2R, PLCB2, CD97, KL, SHC2, AGT, WNT9A, ARHGEF16, OR2A4, ARHGEF17, OR51I2, OR2A1, EGFR, AGT, ARHGEF7, HCRTR1, KISS1R, PIK3R1, PIK3R2, PDPK1, MAP2K2, OR6B1, OR6B2, OR9Q2, CX3CL1, PTAFR, ARHGEF4, ARHGEF3, PDGFA, CCL28, OR2A42, CCL27, PLEKHG5, FGF3, FGF4, GAB2, ITPR1, F2RL3, ITPR3, LPAR1, PIK3CG, ADCY7, RASAL2, PPYR1, WNT1, ADCY9, MC1R, CCL17, KLB, GALR2, PNOC, GPR176, FFAR1, FFAR2, S1PR5, DAGLA, CSF2RA, NPBWR2, NPBWR1, GRIN2D, TRPC7, ADRBK1, TAS1R3, SSTR4, GHRL, ADORA3, SSTR2, SSTR3, NRG2, RLN3. HIST1H3F, BRD1, HDAC3, HIST1H2BG, SMARCA4, HIST1H2BK, KDM5B, MLL2, EZH2, MLL4, ACTL6B, DNMT3A, MTA3, HCFC1, EATS4, YEATS2, PRMT5, KDM4A, MORF4L2, HIST1H4E, ARID1B, HIST1H4D, TADA2B, C12orf41, HIST1H2AL. DR1, HIST1H2BI, CHD3, KDM3B, CHD4, MLL, TRRAP, HIST1H3D, KDM5C, SAP130, HIST1H3E, PADI2, PADI6, MTA1, PRDM16, PADI1, TRRAP, KIAA1267, NSD1, KDM4B, HIST1H4L, SMARCD3, EP400, RUVBL2, SUPT3H, DOT1L,SUZ12P, KAT2A, FAM48A, HIST2H4B, WHSC1, GATAD2A, KDM5C, SUV39H2, ASH2L, HIST3H3, NCOR2, HDAC10, JAK2, EHMT1, CSRP2BP, KDM6B, PRMT7, CREBBP, KDM6B, HIST3H3, SETD3, RBP1, SETD1B, SETD7, ING5, SMYD2, MBD3, AEBP2, KDM2B, WDR5. (Continued)Immune SystemDNA RepairSignaling by GPCRChromatin organizationPLOS ONE | DOI:10.1371/journal.pone.0157866 June 29,10 /Methylation Landscape of Breast Cancer Cells in Response to ResveratrolTable 2. (Continued) Pathway name Cellular responsesto stress Number of genes 106 Hypermethylated (bold letters) and hypomethylated genes MAPKAPK5, MTMR14, UBE2D1, HIST1H2BG, HSPA2, NUP133, HIST1H2BK, CCS, EZH2, HBXIP, IL8, NUP98, TNIK, GPX7, CABIN1, FZR1, MTOR, ASF1A, HIST1H4E, MAP2K3, HIST1H4D, WDR45L, MAPK10, CBX6, POM121C, MINK1, NECAB3, SCMH1, HSPA12A, EPAS1, HIST1H2AL. HSPA6, HSPA7, HSPA4L, GPX2, HSPA13, GPX1, WIPI2, HIST1H2BI, PC, BAG5, HIST1H3D, MAP1LC3B, HSPA8, HIST1H3E, MAP1LC3A, CDKN.

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