Supplemental Information Biological and Pharmaceutical Bulletin Promoter Methylation Profiles between Human Lung Adenocarcinoma Multidrug Resistant A549/Cisplatin (A549/DDP) Cells and Its Progenitor A549 Cells Ruiling Guo, Guoming Wu, Haidong Li, Pin Qian, Juan Han, Feng Pan, Wenbi Li, Jin Li, and Fuyun Ji © 2013 The Pharmaceutical Society of Japan Table S1. Gene categories involved in biological functions with hypomethylated promoter identified by MeDIP-ChIP analysis in lung adenocarcinoma MDR A549/DDP cells compared with its progenitor A549 cells Different biological Genes functions transcription factor MYOD1, CDX2, HMX1, THRB, ARNT2, ZNF639, HOXD13, RORA, FOXO3, HOXD10, CITED1, GATA1, activity HOXC6, ZGPAT, HOXC8, ATOH1, FLI1, GATA5, HOXC4, HOXC5, PHTF1, RARB, MYST2, RARG, SIX3, FOXN1, ZHX3, HMG20A, SIX4, NR0B1, SIX6, TRERF1, DDIT3, ASCL1, MSX1, HIF1A, BAZ1B, MLLT10, FOXG1, DPRX, SHOX, ST18, CCRN4L, TFE3, ZNF131, SOX5, TFEB, MYEF2, VENTX, MYBL2, SOX8, ARNT, VDR, DBX2, FOXQ1, MEIS3, HOXA6, LHX2, NKX2-1, TFDP3, LHX6, EWSR1, KLF5, SMAD7, MAFB, SMAD5, NEUROG1, NR4A1, NEUROG3, GSC2, EN2, ESX1, SMAD1, KLF15, ZSCAN1, VAV1, GAS7, USF2, MSL3, SHOX2, DLX2, ZNF215, HOXB2, LASS3, HOXB5, ETS2, LASS2, DLX5, TCF12, BACH2, ZNF18, TBX21, E2F8, PRRX1, ZNF154, CTCF, PAX3, PRRX2, CBFA2T2, FEV, FOS, BARX1, PCGF2, SOX15, NFIL3, RBPJL, FOSL1, ALX1, EGR3, SOX14, FOXJ1, ZNF92, OTX1, ESR1, ZNF142, FOSB, MIXL1, PURA, ZFP37, ZBTB25, ZNF135, HOXC13, KCNH8, ZNF483, IRX4, ZNF367, NFIX, NFYB, ZBTB16, TCF7L1, HIC1, TSC22D1, TSC22D2, REXO4, POU3F2, MYOG, NFATC2, ENO1, HSFX1, TBX3, CEBPD, CREB1, TBX5, TRIM28, LMX1A, VSX1, HIF3A, IRF4, PBX2, ZNF256, MESP2, FOXE3, NFIB plasma membrane part DLC1, CADM3, VAPA, CADM1, AQP5, SYT9, RAB1B, CD52, SYT6, GRIN3B, RCE1, AQP1, AQP2, ZNRF2, SYP, AGTR1, S1PR3, KCNK6, GNG3, HTR1E, PTPRJ, PLD2, EFNB3, GPER, PTPRG, MDGA1, CD40, MYH9, PTPRO, SSTR4, CRHR1, RND2, CRHR2, SSTR2, EGFLAM, PGM5, RHCG, CD34, HTR6, RAB14, PDGFRA, PDGFRB, LAMC2, HAS3, PMP22, HS3ST3B1, DCBLD2, ORAI1, ENPP1, GNAI1, ASZ1, CACNB1, ADRBK1, EPHB1, ITGBL1, DUSP15, GIT1, TRPC4, SMAD7, MAOA, NPY5R, CAMK2N1, NOTCH3, NTRK3, GNGT2, FNBP1, PKP1, EPHA8, RAPSN, NTRK1, NLGN4X, AVPR1B, NTRK2, RHEB, SLC46A1, KCNH1, PCDHA7, TOLLIP, SLC20A2, MYO7A, KCNIP2, GJA4, INSRR, ASGR1, SLC22A4, SYNJ2, HHIP, IL13RA1, KCNG3, SLC22A2, KCNG1, GHR, CTBP2, LYN, CCKBR, RXFP3, MMP16, SIGMAR1, GRM1, LDLRAP1, EPB41L3, SLC26A6, XPR1, DOK7, KCNH6, ADAM17, SGCE, RASD1, PARVA, TF, RAB3C, NPY2R, TFR2, OPRK1, NCF1C, AMPH, SORBS3, SLC4A9, CD24, MICALL2, FLRT2, TRHDE, GPR75, ATRN, FADS2, GJB4, GRIA4, FZD2, SLC16A2, AP2A2, CD19, RAB35, NPHS1, AMOT, RAB39, PTCH2, HTR2C, ENAH, GNA15, GRIK2, GABRB2, TNFSF13, VIPR1, SLC7A6, IL17RB, DMXL2, GPR45, ERAS, MCOLN1, SLC4A3, INSR, SPN, INADL, KCND2, PSD3, SOCS7, STIM1, HLA-B, SLC34A3, ADRM1, TNS1, ARRB1, VAMP5, GPR50, EDA, NEURL2, KIR2DL3, IGSF9, SNTG2, CAV3, SLC38A3, DRD1, FGFR3, DRD5, COPZ1, KEAP1, PCDHAC1, KCNS1, P2RY6, TRO, P2RY1, SCARB1, TRAF7, SLC30A3, PRIMA1, GABRQ, DIXDC1, GABRA2, RAB8B, ADAM23, KCTD19, CD276, CRB3, RAB33A, LAMP1, CORO1A, P2RX1, SLC7A2, SYT13, SLC13A3, HSPD1, SCN8A, ADRA1D, GPR31, CACNA1B, SLC5A3, OPCML, CLDN6, GABBR1, GABBR2, CLTC, LGR5, MBP, GPC4, ACVR1B, SLC1A2, PRMT8, SLC1A6, SNTB1, RHOD, VPS16, ZYX, NRG1, CSK, SV2C, KCNQ1, SLC1A1, DLG1, IRAK1, ANKS1B, PTGER3, LIMK1, ESR1, KTN1, SLC9A3R2, ARHGAP26, CCNL2, GAK, BBS1, OSM, PRKD1, TNFRSF9, SDC1, FOLH1, ULBP3, FAM120A, ARCN1, LCK, CA4, JAM2, TM4SF5, ROM1, CALCR, PRKCZ, FKBP8, TNFRSF25, RHBG, CDH1, TNFRSF4, TPM1, IGF1R, HRH3, RASGRP2, TGM1, INPP5E, SCNN1G, SLC39A4, EHD1, TCIRG1, FLT3, SLC12A5, CD99, FRMPD1, MAL, NUP155, SLC6A7, SCN4B, CHRNA10, F2R, BMPR1A sequence-specific DNA MYOD1, HMX1, CDX2, THRB, HOXD13, RORA, FOXO3, HOXD10, GATA1, HOXC6, ZGPAT, ATOH1, HOXC8, binding FLI1, GATA5, HOXC4, HOXC5, RARB, RARG, SIX3, FOXN1, ZHX3, SIX4, NR0B1, SIX6, DDIT3, ASCL1, HIF1A, MSX1, DPRX, FOXG1, SHOX, TFE3, TFEB, MYEF2, VENTX, ARNT, DBX2, VDR, FOXQ1, MEIS3, HOXA6, LHX2, NKX2-1, LHX6, DNMT3B, EWSR1, MAFB, SMAD7, NR4A1, ESX1, EN2, GSC2, USF2, SHOX2, DLX2, GCM2, HOXB2, LASS3, LASS2, DLX5, ETS2, HOXB5, HSPD1, TCF12, BACH2, PRRX1, CTCF, PRRX2, PAX3, FEV, FOS, BARX1, NFIL3, FOSL1, ALX1, FOXJ1, SOX14, OTX1, ESR1, FOSB, MIXL1, PURA, HOXC13, KCNH8, IRX4, NFIX, NFYB, POU3F2, NFATC2, HSFX1, TBX3, CEBPD, TBX5, CREB1, TRIM28, LMX1A, VSX1, TBL1X, PBX2, FOXE3 transcription regulator CDX2, ZNF639, HOXD13, RORA, HOXD10, SOHLH2, CITED1, MAGED1, ZGPAT, FLI1, SIN3A, WDR77, activity PHTF1, RARB, RARG, ZHX3, HMG20A, MSX1, CAMK4, BAZ1B, MLLT10, FOXG1, DPRX, VGLL2, SHOX, ST18, ZNF382, ZNF131, MYEF2, VENTX, MYBL2, LYL1, LHX2, DNMT3L, NKX2-1, LHX6, DNMT3B, ZNF398, NKRF, KLF5, SMAD7, SMAD5, KLF15, SMAD1, EN2, ZSCAN1, GAS7, USF2, SHOX2, DLX2, ZNF215, TCEB3B, ETS2, DLX5, JAZF1, TCF12, ZNF18, BACH2, TBX21, ZNF154, ZNF345, CCNE1, SIK1, ATF7IP, CTBP2, GMEB2, ZNF142, FOSB, ZFP37, MXD4, ZBTB25, MED7, ZNF135, NAB2, KCNH8, ZNF483, THOC1, POLR2I, ZNF367, ZBTB16, REXO4, TBX3, TBX5, TRIM28, LMX1A, ZNF256, PBX2, FOXE3, TOB1, MYOD1, HMX1, THRB, ARNT2, FOXO3, HOXC6, GATA1, ATOH1, HOXC8, GATA5, HOXC4, HOXC5, ATOH8, MYST2, MYST3, POU2AF1, SIX3, FOXN1, ARID1A, SIX4, NR0B1, SIX6, TRERF1, DDIT3, ELL2, ASCL1, HIF1A, RIPK3, SMARCA1, CCRN4L, TFE3, SOX5, TFEB, UBE2V1, KEAP1, SOX8, ARNT, MED12L, VDR, DBX2, FOXQ1, MEIS3, HOXA6, TFDP3, EWSR1, RFX4, MAFB, NR4A1, NEUROG1, GSC2, ESX1, NEUROG3, VAV1, MSL3, HOXB2, LASS3, LASS2, DYRK1B, HOXB5, DDX54, DNAJB6, E2F8, PRRX1, CTCF, PAX3, PRRX2, PAWR, CBFA2T2, FEV, FOS, BARX1, PCGF2, SOX15, PDE8B, NFIL3, NRG1, FOSL1, RBPJL, ALX1, IRAK1, EGR3, SOX14, FOXJ1, LDB1, ZNF92, OTX1, ESR1, UBE2I, MIXL1, PURA, NCOA3, HOXC13, ZMIZ2, IRX4, NFIX, CDH1, NFYB, TCF7L1, HIC1, TSC22D1, TSC22D2, LBXCOR1, POU3F2, MYOG, NFATC2, GTF3C4, ENO1, NACC2, HSFX1, DTX1, CEBPD, CREB1, VSX1, HIF3A, IRF4, TBL1X, MESP2, NFIB intrinsic to plasma GRIK2, GABRB2, AQP5, TNFSF13, CD52, GRIN3B, RCE1, VIPR1, AQP1, SLC7A6, IL17RB, AGTR1, S1PR3, membrane GPR45, KCNK6, MCOLN1, INSR, SLC4A3, SPN, HTR1E, PTPRJ, KCND2, EFNB3, PTPRG, GPER, MDGA1, STIM1, HLA-B, CD40, MYH9, PTPRO, CRHR1, SSTR4, ADRM1, CRHR2, SSTR2, RHCG, HTR6, PDGFRA, VAMP5, GPR50, PDGFRB, HAS3, EDA, KIR2DL3, HS3ST3B1, DCBLD2, ORAI1, SLC38A3, DRD1, FGFR3, DRD5, EPHB1, PCDHAC1, ITGBL1, KCNS1, P2RY6, TRO, P2RY1, SCARB1, TRAF7, SLC30A3, PRIMA1, GABRQ, TRPC4, ADAM23, KCTD19, NPY5R, NOTCH3, NTRK3, LAMP1, P2RX1, EPHA8, SLC7A2, NTRK1, NTRK2, AVPR1B, NLGN4X, SYT13, SCN8A, ADRA1D, GPR31, SLC5A3, KCNH1, PCDHA7, OPCML, TOLLIP, SLC20A2, GABBR1, GABBR2, GJA4, KCNIP2, LGR5, INSRR, GPC4, ASGR1, ACVR1B, SLC1A6, SLC22A4, ZYX, HHIP, IL13RA1, KCNG3, SLC1A1, KCNQ1, SLC22A2, KCNG1, GHR, IRAK1, PTGER3, LYN, CCKBR, RXFP3, KTN1, MMP16, SIGMAR1, GRM1, CCNL2, PRKD1, OSM, TNFRSF9, SLC26A6, SDC1, FOLH1, XPR1, KCNH6, ADAM17, SGCE, JAM2, TM4SF5, ROM1, CALCR, TNFRSF25, NPY2R, TFR2, OPRK1, RHBG, NCF1C, TNFRSF4, IGF1R, HRH3, CD24, SCNN1G, TCIRG1, FLRT2, TRHDE, FLT3, GPR75, ATRN, FADS2, CD99, MAL, GRIA4, FZD2, SLC16A2, CD19, SLC6A7, NPHS1, SCN4B, PTCH2, CHRNA10, F2R ion transport CALHM1, TSPO, SCN3B, GABRB2, GRIK2, SLC22A15, GRIN3B, AQP1, KCNK7, KCNK6, TPT1, MCOLN1, SLC4A3, FTL, SLC12A8, KCND2, SLC22A23, STIM1, SLC34A3, NNT, KCNT1, RHCG, ORAI1, SLC38A4, SLC38A3, SLC38A2, ENPP1, SLC38A7, CACNB1, ASZ1, SLC38A10, FXYD6, ATP6V0C, VDR, KCNS1, P2RY6, SLC30A3, HCN4, HCN3, GABRQ, HCN1, TRPC4, PRAF2, GABRA2, TRPC6, KCTD19, TST, CORO1A, P2RX1, SLC13A3, SCN8A, CACNA1B, ATP5D, STEAP3, KCNH1, KCNK17, SLC5A3, ATP5E, SLC20A2, ANO1, GJA4, KCNK13, KCNIP2, KCNK10, SLC1A2, SLC1A6, SLC22A4, TRPV4, SLC25A1, ATP5I, KCNG3, SLC1A1, KCNQ1, SLC22A2, KCNG1, TRPM4, PTGER3, TRPM5, TMEM38A, CDK2, ATP6V1F, ATP6V1C2, SLC26A6, SLC26A8, CLIC4, LCK, SLC41A3, KCNH6, KCNH8, STEAP2, KCNH3, TRAPPC10, TF, TFR2, RHBG, FKBP1B, TPCN1, C1QTNF3, FTHL17, SCNN1G, SLC4A9, SLCO3A1, SLC39A4, SLC39A3, KCNE3, TCIRG1, PLP2, SLC12A5, ATP5F1, GRIA4, ZACN, FYN, SCN4B, ABCC8, CHRNA10, F2R integral to plasma GRIK2, GABRB2, AQP5, TNFSF13, CD52, RCE1, GRIN3B, VIPR1, AQP1, SLC7A6, IL17RB, AGTR1, S1PR3, membrane GPR45, KCNK6, MCOLN1, INSR, SLC4A3, SPN, HTR1E, PTPRJ, KCND2, EFNB3, PTPRG, GPER, STIM1, HLA-B, CD40, MYH9, PTPRO, CRHR1, SSTR4, ADRM1, CRHR2, SSTR2, RHCG, HTR6, PDGFRA, VAMP5, GPR50, PDGFRB, HAS3, EDA, KIR2DL3, HS3ST3B1, DCBLD2, ORAI1, SLC38A3, DRD1, FGFR3, DRD5, EPHB1, PCDHAC1, ITGBL1, KCNS1, P2RY6, TRO, P2RY1, SCARB1, SLC30A3, GABRQ, TRPC4, ADAM23, KCTD19, NPY5R, NOTCH3, NTRK3, LAMP1, P2RX1, EPHA8, SLC7A2, NTRK1, NTRK2, AVPR1B, NLGN4X, SYT13, SCN8A, ADRA1D, GPR31, SLC5A3, KCNH1, PCDHA7, OPCML, TOLLIP, SLC20A2, GABBR1, GABBR2, GJA4, KCNIP2, LGR5, INSRR, GPC4, ASGR1, ACVR1B, SLC1A6, SLC22A4, ZYX, HHIP, IL13RA1, KCNG3, SLC1A1, KCNQ1, SLC22A2, KCNG1, GHR, IRAK1, PTGER3, LYN, CCKBR, RXFP3, KTN1, MMP16, SIGMAR1, GRM1, CCNL2, PRKD1, OSM, TNFRSF9, SLC26A6, SDC1, FOLH1, XPR1, KCNH6, ADAM17, SGCE, JAM2, ROM1, TM4SF5, CALCR, TNFRSF25, NPY2R, TFR2, OPRK1, RHBG, NCF1C, TNFRSF4, IGF1R, HRH3, SCNN1G, TCIRG1, FLRT2, TRHDE, FLT3, GPR75, ATRN, FADS2, CD99, MAL, GRIA4, FZD2, SLC16A2, CD19, SLC6A7, NPHS1, SCN4B, PTCH2, CHRNA10, F2R Table S2. Gene categories involved in biological functions with hypermethylated promoter identified by MeDIP-ChIP analysis in lung adenocarcinoma MDR A549/DDP cells compared with its progenitor A549 cells Different biological Genes functions embryonic morphogenesis TWSG1, FGF8, FOXA2, WNT3A, GDF5, HIRA, TGFB3, DSCAML1, ZEB1, ALDH1A2, MACF1, OVOL2, MYO15A, TDGF1, MKKS, IPMK, FRS2, TBX6, RET, SATB2, TBX15, GSC, TGFBR1, SMAD3, SIX2, SKI, SMAD2, CELSR1, SOD1, HOXC10, EYA2, HOXC11, ITGA8, HOXD3, DLD, HOXD4, FOXE1, LRP6, TFAP2A, FOXC1, APAF1, WNT9A, NSD1, MAB21L2, WNT7A, SMARCA4 gastrulation TWSG1, TBX6, FGF8, GSC, FOXA2, WNT3A, HIRA, SMAD3, SMAD2, EYA2, MACF1, DLD, TDGF1, LRP6, MKKS, FOXC1, NSD1, FRS2 .