Table 2.
Categorization of differentially methylated (DM) Promoter CpGs in KRAS-inhibited most responsive cell lines (Pa16C, Pa01C, PANC-1 and Panc 10.05 cells).
| Pa16C cells | Pa01C cells | PANC-1 cells | Panc 10.05 cells | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Hyper- methylated |
Hypo- methylated |
Hyper- methylated |
Hypo- methylated |
Hyper- methylated |
Hypo- methylated |
Hyper- methylated |
Hypo- methylated |
||||||
| Transcription Factors | |||||||||||||
| ASCL2 | PFDN5 | ARNT | HOXD8 | SMARCA5 | ALX1 | ALX4 | PAX7 | ID3 | AIRE | LSR | ASCL1 | BNC2 | LHX4 |
| CBX4 | RAX | ATOH7 | INSM2 | TAF3 | ALX3 | BARHL2 | PDX1 | KLF14 | CUX2 | MAF | BRF1 | C13orf15 | LIN28A |
| CRIP1 | RING1 | BACH2 | IRF7 | THRB | EZH1 | BHLHE22 | PHOX2A | MLLT6 | EBF4 | NEUROG1 | MKX | CASZ1 | LYL1 |
| E2F2 | RREB1 | BAZ2B | IRX1 | TMF1 | HMGB2 | BNC1 | PHOX2B | MSX2 | EGR3 | NFATC4 | NEUROG1 | CBFA2T3 | MSC |
| EBF4 | SALL4 | BRF1 | IRX2 | TRIM13 | HMX2 | BRF1 | PITX2 | NKX2-5 | EMX1 | NKX2-6 | ZFP30 | ESR2 | MSX1 |
| ELK3 | SIX3 | BTF3 | LIN28A | TRIM27 | HOXB1 | DBX1 | PLAGL1 | NKX3-1 | ETV7 | NKX6-2 | EVX2 | PAX7 | |
| EOMES | TCF7 | CECR6 | LMX1B | TSC22D2 | IRX1 | DBX2 | PRDM13 | PAX1 | FOXA2 | NRIP1 | FEZF2 | PCGF3 | |
| EYA2 | TLX2 | CNPY3 | MED24 | TSHZ3 | KDM3B | DLX1 | RNF2 | PRDM8 | FOXB1 | PBX4 | FOXE3 | RARG | |
| FOXC2 | TUB | CSRP1 | MIXL1 | TWIST1 | LHX8 | DMRT1 | RORB | TBX2 | FOXD3 | PER1 | FOXI1 | RUNX3 | |
| FOXE1 | TULP1 | CSRP2 | MKX | ULK2 | NEUROG1 | DMRTA2 | RUNX3 | TCF7L2 | FOXF1 | PHF11 | GBX2 | SALL1 | |
| GBX1 | UNCX | CUX2 | MSX2P1 | UTF1 | NKX2-2 | ESR1 | SALL3 | YAF2 | GATA5 | PITX3 | GSC | SALL3 | |
| GSX1 | VENTX | ELK4 | NCALD | VAX1 | PAX3 | EYA4 | TBX3 | ZNF213 | GFI1 | POU3F1 | HKR1 | T | |
| HAND1 | ZAR1 | EN1 | NEUROG1 | VSX1 | SOX8 | FEZF2 | TCF4 | ZNF222 | GSC2 | RARA | HOXA9 | TLX3 | |
| HAND2 | ZBTB16 | ERMP1 | NEUROG3 | YBX2 | TLX2 | FOXB1 | ULK2 | GSX1 | RAX | HOXB13 | TUB | ||
| HES2 | ZFP28 | ESR1 | NFYC | ZBTB22 | TWIST1 | GBX2 | ZIC1 | HAND1 | RORB | HOXB2 | VEZF1 | ||
| HNF1A | ZSCAN12 | ESRRG | OLIG1 | ZFP30 | ZNF213 | GCM2 | ZNF16 | HAND2 | SIM2 | HOXB4 | ZBTB16 | ||
| HOXB1 | EYA4 | PDLIM5 | ZIC1 | ZNF593 | GFI1 | ZNF18 | HES4 | SIX2 | HOXB8 | ZBTB17 | |||
| HOXC10 | FOXE3 | PHOX2A | ZMYND11 | HIC1 | ZNF256 | HEYL | TBX5 | IRX2 | ZFP28 | ||||
| HOXC4 | FOXG1 | PLAGL1 | ZNF124 | HOXA6 | ZNF331 | HLX | THRB | IRX3 | ZIC1 | ||||
| HOXD12 | GBX2 | POU3F2 | ZNF135 | HOXA9 | HMX3 | TOX | LEF1 | ZNF236 | |||||
| HOXD3 | GLI3 | POU4F1 | ZNF18 | HOXB13 | HNF1A | VENTX | |||||||
| HOXD4 | GRHL1 | PPARG | ZNF207 | HOXB2 | HNF1B | WT1 | |||||||
| HOXD9 | HIF3A | PRDM13 | ZNF211 | HOXC9 | HOXC13 | YBX2 | |||||||
| IRF4 | HMX3 | PRDM14 | ZNF219 | HOXD3 | HOXD1 | ZAR1 | |||||||
| KCNIP3 | HOXA5 | PRDM6 | ZNF232 | ID4 | HR | ZFP37 | |||||||
| MYCNOS | HOXA9 | RARG | ZNF268 | IRF7 | IRF6 | ZNF229 | |||||||
| NEUROG2 | HOXB13 | RBBP9 | ZNF295 | MKX | IRF8 | ZNF334 | |||||||
| NFIC | HOXB3 | RUNX3 | ZNF318 | MSC | ISL1 | ZNF701 | |||||||
| NKX6-1 | HOXB4 | SALL1 | ZNF532 | MSX1 | LEF1 | ZSCAN12 | |||||||
| NKX6-3 | HOXB8 | SALL3 | ZNF682 | NKX2-5 | |||||||||
| OSR1 | HOXC8 | SAMD4B | NKX6-2 | ||||||||||
| OTP | HOXD1 | SIM2 | PAX1 | ||||||||||
| Cytokines & Growth Factors | |||||||||||||
| BDNF | LEFTY1 | BMP3 | FGF2 | NRG3 | FGF20 | CALCA | GRP | CXCL5 | BMP2 | LTBP2 | CALCA | CMTM2 | SCT |
| CALCA | LTBP3 | CCK | FGF20 | PTHLH | GDF6 | CMTM2 | HAMP | KL | BMP7 | MDK | CCK | FGF2 | SEMA5A |
| CSF1 | PDGFRA | CMTM1 | FGF5 | SEMA6D | IL28B | EPO | NGF | BMP8A | NGF | GRP | SLIT1 | ||
| CXCL12 | PENK | CMTM3 | FGF9 | SLIT1 | NRG3 | FGF11 | PSPN | CXCL16 | NRG1 | NPY | |||
| FGF19 | PTH2 | DKK1 | GDNF | TNFSF13 | PDGFA | FGF12 | SEMA5A | EDN3 | NRG3 | ||||
| GDF7 | SCGB3A1 | EPO | GREM1 | SEMA6B | FGF2 | SLIT1 | FAM3B | RLN3 | |||||
| KL | SECTM1 | FGF11 | KITLG | GREM1 | SLIT2 | FGF22 | STC2 | ||||||
| FGF6 | TNFSF12 | ||||||||||||
| GDF10 | TYMP | ||||||||||||
| GDF7 | VEGFC | ||||||||||||
| GRP | |||||||||||||
| Homeodomain Proteins | |||||||||||||
| GBX1 | NKX6-1 | CUX2 | HOXC8 | POU3F2 | ALX1 | ALX4 | HOXD3 | MSX2 | CUX2 | ISL1 | MKX | EVX2 | HOXB8 |
| GSX1 | NKX6-3 | EN1 | HOXD1 | POU4F1 | ALX3 | BARHL2 | MKX | NKX2-5 | EMX1 | NKX2-6 | GBX2 | IRX2 | |
| HNF1A | OTP | GBX2 | HOXD8 | TSHZ3 | HMX2 | DBX1 | MSX1 | NKX3-1 | GSC2 | NKX6-2 | GSC | IRX3 | |
| HOXB1 | RAX | HMX3 | IRX1 | VAX1 | HOXB1 | DBX2 | NKX2-5 | GSX1 | PBX4 | HOXA9 | LHX4 | ||
| HOXC10 | SIX3 | HOXA5 | IRX2 | VSX1 | IRX1 | DLX1 | NKX6-2 | HLX | PITX3 | HOXB13 | MSX1 | ||
| HOXC4 | TLX2 | HOXA9 | LMX1B | LHX8 | GBX2 | PAX7 | HMX3 | POU3F1 | HOXB2 | PAX7 | |||
| HOXD12 | UNCX | HOXB13 | MIXL1 | NKX2-2 | HOXA6 | PDX1 | HNF1A | RAX | HOXB4 | TLX3 | |||
| HOXD3 | VENTX | HOXB3 | MKX | PAX3 | HOXA9 | PHOX2A | HNF1B | SIX2 | |||||
| HOXD4 | HOXB4 | MSX2P1 | TLX2 | HOXB13 | PHOX2B | HOXC13 | VENTX | ||||||
| HOXD9 | HOXB8 | PHOX2A | HOXB2 | PITX2 | HOXD1 | ||||||||
| HOXC9 | |||||||||||||
| Protein Kinases | |||||||||||||
| CAMK2B | PDGFRA | AATK | MAPK7 | PINK1 | CDK6 | CDKL3 | BRAF | ACVR1C | KDR | PRKAA2 | CDC42BPB | NEK3 | |
| FASTK | STK19 | BRAF | MYO3A | SGK1 | DDR1 | DCLK2 | CSNK1A1 | BCR | KSR2 | RIPK3 | FGFR1 | NTRK3 | |
| HUNK | TNK2 | CDC42BPB | NEK10 | SNRK | EIF2AK2 | NEK9 | CDKL2 | MAST4 | |||||
| KDR | CDKL3 | NEK3 | STYK1 | HIPK3 | PDK2 | CSNK1G2 | MST1R | ||||||
| LCK | FGFR1 | NRBP1 | ULK2 | MAP2K1 | PINK1 | DAPK1 | PBK | ||||||
| MAP3K6 | FGR | NTRK3 | MAPK4 | RIOK3 | DMPK | STK32A | |||||||
| MAPK12 | FYN | PBK | MATK | ULK2 | EPHA6 | STK32B | |||||||
| PRKD1 | FGFR1 | STK33 | |||||||||||
| RYK | FLT3 | SYK | |||||||||||
| HCK | TNK1 | ||||||||||||
| HUNK | WNK2 | ||||||||||||
| INSR | |||||||||||||
| Oncogenes | |||||||||||||
| CCND2 | ZBTB16 | ARNT | GAS7 | PPARG | CCND2 | HOXA9 | BRAF | BCR | KDR | CBFA2T3 | NTRK3 | ||
| IRF4 | BRAF | GNAS | TOP1 | CDK6 | PAX7 | CCND1 | CDH11 | MAF | FGFR1 | PAX7 | |||
| KDR | ELK4 | HOXA9 | TRIM27 | JAK2 | ZNF331 | MLLT6 | DDX6 | PER1 | HOXA9 | TLX3 | |||
| LCK | FGFR1 | HSP90AB1 | JAK3 | FGFR1 | RARA | LYL1 | ZBTB16 | ||||||
| PDGFRA | FIP1L1 | NTRK3 | PAX3 | FLT3 | SEPT9 | ||||||||
| TCL1A | HOXC13 | SYK | |||||||||||
| Cell Differentiation Markers | |||||||||||||
| CD40 | PROM1 | ADAM17 | IL17RA | TNFRSF10B | DDR1 | CD248 | PVRL2 | CDH1 | INSR | FGFR1 | TNFRSF1B | ||
| CD81 | FGFR1 | ITGB3 | TNFRSF8 | NCAM1 | CDH2 | CDH2 | KDR | IFITM1 | |||||
| IL10RA | FZD10 | MME | TNFSF13 | TNFRSF8 | FGFR1 | LAMP3 | |||||||
| KDR | IFITM1 | NGFR | FLT3 | MME | |||||||||
| PDGFRA | IGF2R | FZD10 | MST1R | ||||||||||
| GP1BB | THBD | ||||||||||||
| ICOSLG | |||||||||||||
| Tumor Suppressors | |||||||||||||
| EXT2 | BRCA1 | PHOX2B | BRCA1 | WT1 | FANCA | ||||||||
| HNF1A | CDH1 | XPA | |||||||||||
| HNF1A | |||||||||||||