Table I.
GO enrichment for methylation-related differentially expressed genes.
| A, Downregulated/hypermethylated genes | |||
|---|---|---|---|
| GO ID | GO term | FDR | Genes |
| 0051605 | Protein maturation by peptide bond cleavage | 2.87×10−2 | CFP, C8B, C7, FCN3, KLKB1, C1R |
| 0048545 | Response to steroid hormone stimulus | 1.47×10−2 | PRSS8, FOS, GOT1, CCL2, ACADS, WFDC1, CA2, NPY1R, GHR |
| 0046395 | Carboxylic acid catabolic process | 2.18×10−2 | ASPA, GOT1, ACADS, IDO2, KMO, UROC1, PON3 |
| 0045087 | Innate immune response | 2.26×10−3 | CFP, C8B, C7, FCN3, IL1RAP, VNN1, C1R, CD1D, GCH1 |
| 0031960 | Response to corticosteroid stimulus | 2.93×10−2 | PRSS8, FOS, GOT1, CCL2, ACADS, GHR |
| 0019439 | Aromatic compound catabolic process | 2.70×10−2 | EPHX2, IDO2, KMO, PON3 |
| 0016054 | Organic acid catabolic process | 2.18×10−2 | ASPA, GOT1, ACADS, IDO2, KMO, UROC1, PON3 |
| 0010817 | Regulation of hormone levels | 4.64×10−2 | ALDH8A1, SHBG, LY6E, CRHBP, CYP26A1, SRD5A1, BCO2 |
| 0009725 | Response to hormone stimulus | 2.54×10−2 | PRSS8, FOS, GOT1, CCL2, HMGCS2, ACADS, FBP1, WFDC1, CA2, NPY1R, GHR |
| 0009719 | Response to endogenous stimulus | 4.10×10−2 | PRSS8, FOS, GOT1, CCL2, HMGCS2, ACADS, FBP1, WFDC1, CA2, NPY1R, GHR |
| 0009611 | Response to wounding | 1.02×10−3 | C7, CCL2, HPS5, EPHX2, CHST4, C1R, CFP, C8B, FOS, LPA, PLSCR4, FCN3, KLKB1, IL1RAP, PROZ, VNN1, NGFR |
| 0006959 | Humoral immune response | 2.46×10−2 | CFP, C8B, C7, CCL2, FCN3, C1R |
| 0006956 | Complement activation | 2.70×10−2 | CFP, C8B, C7, FCN3, C1R |
| 0006955 | Immune response | 6.96×10−3 | C7, CCL2, CHST4, C1R, VIPR1, CXCL12, CD1D, GCH1, CFP, C8B, FCN3, HAMP, IL1RAP, VNN1 |
| 0006954 | Inflammatory response | 5.26×10−3 | CFP, C8B, FOS, C7, CCL2, FCN3, KLKB1, IL1RAP, EPHX2, VNN1, C1R, CHST4 |
| 0006952 | Defense response | 1.98×10−2 | C7, CCL2, EPHX2, CHST4, C1R, CD1D, GCH1, CFP, C8B, FOS, FCN3, HAMP, KLKB1, IL1RAP, VNN1 |
| 0006575 | Cellular amino acid derivative metabolic process | 2.47×10−2 | GGT5, LY6E, IDO2, VNN1, KMO, BBOX1, GHR, GCH1 |
| 0002526 | Acute inflammatory response | 3.37×10−3 | CFP, C8B, C7, FCN3, KLKB1, EPHX2, VNN1, C1R |
| B, Upregulated/hypomethylated genes | |||
| GO ID | GO term | FDR | Genes |
| 0051726 | Regulation of cell cycle | 3.52×10−2 | TP53BP2, NUSAP1, SFN, CDKN3, UBE2C |
| 0051301 | Cell division | 4.37×10−2 | RAD21, NUSAP1, NDC80, PARD3B, CEP55, UBE2C, CDCA3 |
| 0022616 | DNA strand elongation | 4.65×10−2 | RFC4, FEN1 |
| 0022403 | Cell cycle phase | 3.99×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, CDKN3, UBE2C, CDCA3 |
| 0022402 | Cell cycle process | 2.27×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, CDKN3, UBE2C, CDCA3 |
| 0007067 | Mitosis | 3.63×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, UBE2C, CDCA3 |
| 0007049 | Cell cycle | 3.98×10−2 | RAD21, TP53BP2, E2F8, NUSAP1, NDC80, AURKA, PARD3B, CEP55, CDKN3, UBE2C, CDCA3, MCM6 |
| 0006271 | DNA strand elongation during DNA replication | 4.22×10−2 | RFC4, FEN1 |
| 0006261 | DNA-dependent DNA replication | 4.56×10−2 | RFC4, MCM4, FEN1, MCM6 |
| 0006260 | DNA replication | 4.15×10−2 | RFC4, RNASEH2A, MCM4, FEN1, MCM6 |
| B, Upregulated/hypomethylated genes | |||
| GO ID | GO term | FDR | Genes |
| 000028 | Nuclear division | 3.63×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, UBE2C, CDCA3 |
| 0000279 | M phase | 4.61×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, UBE2C, CDCA3 |
| 0000278 | Mitotic cell cycle | 3.06×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, CDKN3, UBE2C, CDCA3 |
| 0000087 | M phase of mitotic cell cycle | 2.68×10−2 | RAD21, NUSAP1, NDC80, AURKA, CEP55, UBE2C, CDCA3 |
FDR, false discovery rate; GO, Gene Ontology.