Table 4.
KEGG Pathway Analysis of Hypermethylated and Hypomethylated Genes
| Pathyway Name | ID | Gene | EntrezGene | Statistic |
|---|---|---|---|---|
| A, KEGG pathway analysis of hypermethylated genes | ||||
| Oxytocin signaling pathway | 04921 | 22 | ADCY4,ADCY2,CACNA2D4,MEF2C,PPP1CC,PIK3R2,TRPM2,PPP1R12C,MAP2K2,ADCY8,NRAS,MAPK7,PLCB2,EGFR,ADCY7,KCNJ9,KCNJ6,OXT,CACNG3,CACNG7,CACNG8,FOX | C=159 O=22 P=1.19E-03 |
| Estrogen signaling pathway | 04915 | 14 | ADCY4,ADCY2,ADCY8,ADCY7,EGFR,AK72,FOS,GPER1,KCNJ6,KCNJ9,NRAS,PIK3R2,PLCB2,MAP2K2 | C=100 O=14 P=5.91E-03 |
| Notch signaling pathway | 04330 | 9 | RBPJL,CTBP1,DTX1,HES5,JAG2,NOTCH4,NUMBL,NCOR2,MAML1 | C=48 O=9 P=9.04E-03 |
| Signaling pathways regulating pluripotency of stem cells | 04550 | 17 | DLX5,APC2,AKT2,FGFR3,JAK2,JAK3,ZFHX3,NRAS,MAPK11,REST,MAP2K2,FIK3R2,BMPR11A,WNT10A,FZD1,WNT5B,HAND1 | C=142 O=17 P=1.26E-02 |
| Endometrial cancer | 05213 | 8 | CTNNA1,APC2,EGFR,AKT2,NRAS,FIK3R2,MAP2K2,CDH1 | C=52 O=8 P=1.39E-02 |
| Rap1 signaling pathway | 04015 | 22 | ADCY4,EPHA2,RASGRP2,EFNA5,RAPGEF3,ADCY8,RGS14,EGFR,ADCY2,ADCY7,AKT2,FGFR3,PFN3,NRNAS,RALGDS,FIK3R2,RALB,RALA,MAP2K2,MAPK11,PLCB2,CDH1 | C=211 O=22 P=1.41E-02 |
| Prolactin signaling pathway | 04917 | 10 | AKT2,FOS,JAK3,NRAS,FIK3R2,MAPK11,MAP2K2,TNFRSF11A,SOCS6,SOCS3 | C=72 O=10 P=1.52E-02 |
| Adrenergic signaling in cardiomyocytes | 04261 | 17 | ADCY7,ADCY4,CACNG3,RAPGEF3,ADCY2,ADCY8,ADRA1A,AKT2,ATP2B1,PPP1CC,MAPK11,CACNG8,PIK3R2,PLCB2,CACNG7,TPM1,CACNA2D4 | C=149 O=1 7 1.88E-02 |
| Progesterone-mediated oocyte maturation | 04914 | 11 | ADCY4,ADCY2,ADCY8,ADCY7,AKT2,RPS6KA6,MAPK11,FIK3R2,RPS6KA2,MAPD1L1,CCNA1 | C=86 O=11 P=2.06E-02 |
| Inflammatory mediator regulation of TRP channels | 04750 | 11 | ADCY2,ADCY8,ADCY7,ALOX12,ADCY4,PRKCH,PPP1CC,MAPK11,FIK3R2,PLCB2,PRKCE | C=99 O=11 P=2.45E-02 |
| Cholinergic synapse | 04725 | 13 | ADCY4,CHAT,ADCY2,ADCY8,ADCY7,AKT2,FOS,KCNJ6,JAK3,NRAS,FIK3R2,PLCB2,SLC18A3 | C=113 O=13 P=2.98E-02 |
| Adherens junction | 04520 | 9 | SORBS1,BAIAP2,EGFR,CTNNA1,LMO7,PTPRM,ACP1,ACTN4,CDH1 | C=73 O=9 P=3.61E-02 |
| SNARE interactions in vesicular transport | 04130 | 4 | GOSR2,STX2,VAMP2,STX5 | C=34 O=4 P=3.83E-02 |
| Transcriptional misregulation in cancer | 05202 | 18 | FLI1,HOXA11,HOXA9,HOXA10,MLLT1,H3F3C,MEF2C,PAX7,PAX5,SPINT1,RXRA,HIST2H3D,PAX8,ZBTB16,WT1,ZBTB17,HIST1H3D,CCNA1 | C=179 O=18 P=4.59E-02 |
| Long-term potentiation | 04720 | 9 | RAPGEF3,ADCY8,RPS6KA6,GRIN2D,NRAS,PPP1CC,PLCB2,MAP2K2,RPS6KA2 | C=67 O=9 P=4.97E-02 |
| C, the number of reference genes in the category; O is the number of genes in the gene set and also in the category, p-value from hypergeometric test | ||||
| B, KEGG pathway analysis of hypomethylated genes | ||||
| Endometrial cancer | 05213 | 9 | EGFR,CTNNA2,FOXO3,AKT1,CCND1,PIK3CD,MAP2K2,TCF7 | C=52 O=9 P=8.51E-04 |
| Nicotine addiction | 05033 | 10 | GRIN3B,GRIN3A,GRIN2A,GRIN2D,GRIN2C,GRIN1,GABRD,GABRA5,GABRB3,CACNA1A | C=40 O=10 P=1.35E-03 |
| Glioma | 05214 | 10 | CDKN2A,EGFR,AKT1,CALML5,PDGFA,MAP2K2,SHC3,CCND1,PIK3CD,CAMK2B | C=65 O=10 P=4.33E-03 |
| Acute myeloid leukemia | 05221 | 8 | CEBPA,AKT1,MAP2K2,CCND1,PIK3CD,TCF7,RUNX1,CCNA1 | C=57 O=8 P=4.62E-03 |
| Signaling pathways regulating pluripotency of stem cells | 04550 | 17 | DUSP9,AKT1,NEUROG1,ISL1,ID4,OTX1,MAPK11,MAP2K2,PIK3CD,LHX5,ZIC3,FZD3,WNT5A,WNT7B,AXIN2,WNT5B,WNT10A | C=142 O=17 P=4.96E-03 |
| Proteoglycans in cancer | 05205 | 23 | FLNC,AKT1,CTTN,ANK1,GPC1,EGFR,IGF2,HOXD10,MAPK11,MAP2K2,PIK3CD,PLCE1,CCND1,TGFB1,FZD3,WNT5A,ACTG1,WNT7B,KDR,CAMK2B,WNT5B,WNT10A,HPSE2 | C=204 O=23 P=5.04E-03 |
| Amphetamine addiction | 05031 | 12 | GRIN3B,GRIN3A,GRIN2A,GRIN2D,ARC,GRIN2C,GNAS,GRIN1,CALML5,PPP3CC,CAMK2B,CREB5 | C=68 O=12 P=5.93E-03 |
| Calcium signaling pathway | 04020 | 21 | ADORA2A,ADORA2B,CRIN2A,CRIN2D,GNAS,GNAL,GRIN2C,GRIN1,GRM5,HTR5A,NTSR1,PPP3CC,PLCE1,CALML5,P2RX1,RYR1,CACNA1A,CAMK2B,EGFR,CACNA1H,ORAI3 | C=180 O=21 P=7.79E-03 |
| Melanoma | 05218 | 7 | CNKN2A,EGFR,AKT1,PDGFA,MAP2K2,CCND1,PIK3CD | C=71 O=7 P=7.96E-03 |
| Chronic myeloid leukemia | 05220 | 10 | CTBP1,CNKN2A,CTBP2,SHC3,AKT1,MAP2K2,CCND1,PIK3CD,CAMK2B,TGFB1 | C=73 O=10 P=9.59E-03 |
| Rap1 signaling pathway | 04015 | 20 | ADORA2A,EGFR,EFNA2,ADORA2B,GRIN2A,GNAS,AKT1,GRIN1,KDR,INSR,NGF,MAPK11,MAP2K2,PIK3CD,PLCE1,CALML5,PRKCI,PDGFA,ACTG1,LPAR2 | C=211 O=20 P=1.29E-02 |
| Long-term potentiation | 04720 | 10 | GRIN2A,GRIN2D,GRIN2C,GRIN1,GRM5,CALML5,PPP3CC,MAP2K2,RPS6KA2,CAMK2B | C=67 O=10 P=1.29E-02 |
| Neuroactive ligand-receptor interaction | 04080 | 29 | GRIN3B,DRD4,CHRNE,ADORA2A,HEH3,GPR156,ADRA2A,ADORA2B,GRIN3A,GRM5,GRIN1,GABRD,GABRB3,GRIN2C,P2RY8,GRM6,NPBWR1,GRIN2D,GRIN2A,GABRA5,GRIK4,HTR5A,OPRL1,NTSR1,P2RY11,PRSS3,P2RX1,S1PR4,LPAR2 | C=275 O=29 P=1.84E-02 |
| Non-small cell lung cancer | 05223 | 7 | EGFR,CNKN2A,FOXO3,AKT1,MAP2K2,CCND1,PIK3CD | C=56 O=7 P=2.59E-02 |
| Wnt signaling pathway | 04310 | 16 | CSNK1A1,CTBP2,WIF1,CTBP1,NFATC1,LRP6,CCND1,PPP3CC,TCF7,FZD3,WNT5A,WNT7B,WNT5B,WNT10A,CAMK2B,AXIN2 | C=140 O=16 P=2.97E-02 |
| Pathways in cancer | 05200 | 26 | CEBPA,CNKN2A,CTNNA2,EGFR,CTBP2,DAPK3,CTBP1,EPAS1,AKT1,GSTP1,MAH2,PIK3CD,MAP2K2,CCND1,PDGFA,TGFB1,TCF7,WNT5A,TRAF3,FZD3,WNT7B,CAMK2B,WNT5B,AXIN2,CCNA1,WNT10A | C=327 O=26 P=3.44E-02 |
| Hippo signaling pathway | 04390 | 17 | WTIP,GDF7,DLG1,CTNNA2,AMH,SCRIB,CCND1,TCF7,WNT5A,TGFB1,FZD3,WNT7B,ACTG1,AXIN2,WNT10A,WNT5B,PRKCI | C=154 O=17 P=3.47E-02 |
| MAPK signaling pathway | 04010 | 22 | DUSP5,EGFR,DUSP9,DUSP8,AKT1,MAPK8IP3,FLNC,ARRB1,MAPT,NFATC3,MEF2C,NGF,MAPK11,PPP3CC,MAP2K2,ARRB2,PDGFA,RPS6KA2,TGFB1,CACNA1A,CACNB1,CACNA1H | C=257 O=22 P=3.53E-02 |
| Cocaine addiction | 05030 | 8 | GRIN3B,GRIN3A,GRIN1,GNAS,GRIN2C,GRIN2D,GRIN2A,CREB5 | C=50 O=8 P=3.54E-02 |
| cAMP signaling pathway | 04024 | 20 | GRIN3B,HCN4,ADORA2A,GRIN3A,GRIN1,AKT1,GRIN2C,AMH,GNAS,GRIN2D,GRIN2A,NFATC3,MAP2K2,PIK3CD,PLCE1,CALML5,PDE4D,ACOX3,CAMK2B,CREB5 | C=200 O=20 P=3.64E-02 |
| Amyotrophic lateral sclerosis (ALS) | 05014 | 7 | GRIN2D,GRIN2C,GRIN1,GRIN2A,MAPK11,PRPH,PPP3CC | C=51 O=7 P=3.86E-02 |
| Prolactin signaling pathway | 04917 | 8 | CISH,FOXO3,AKT1,MAPK11,MAP2K2,SHC3,CCND1,PIK3CD | C=72 O=8 P=4.25E-02 |
| Colorectal cancer | 05210 | 7 | AKT1,MSH2,CCND1,PIK3CD,TGFB1,AXIN2,TCF7 | C=62 O=7 P=4.27E-02 |
| Oxytocin signaling pathway | 04921 | 15 | EEF2,EGFR,GNAS,MEF2C,NFATC3,PIK3CD,CCND1,MAP2K2,PPP3CC,CALML5,OXT,RYR1,ACTG1,CACNB1,CAMK2B | C=159 O=15 P=4.41E-02 |
| Glutamatergic synapse | 04724 | 14 | GRIN3B,GRIN3A,GRM6,GRM5,GRIN1,SHANK2,GNAS,GRIN2C,GRIN2D,GRIN2A,GRIK4,PPP3CC,CACNA1A,SHANK3 | C=116 O=14 P=4.72E-02 |
| Axon guidance | 04360 | 14 | SEMA4D,DPYSL2,SEMA6B,EFNA1,EPHA7,LRRC4C,PPP3CC,PLXNA3,SEMA5B,PLXNB3,SLIT1,CXCL12,SEMA3B,NTNG2 | C=127 O=14 P=4.73E-02 |
Abbreviations: C, the number of reference genes in the category; O is the number of genes in the gene set and also in the category, p-value from hypergeometric test.