Table 3.
Gene set enrichment analysis of genes associated with differentially methylated CpG sites.
| Gene sets | Number of genes | Enrichment score | Normalized enrichment score | P value | q value |
|---|---|---|---|---|---|
| Signal transduction pathways | |||||
| Regulation of insulin like growth factor transport and uptake by insulin like growth factor binding proteins (Reactome) | 15 | 0.770 | 1.538 | 0.0024 | 1 |
| TRK receptor signaling mediated by the MAPK pathway (PID) | 18 | 0.740 | 1.528 | 0.0049 | 1 |
| β3 integrin cell surface interactions (PID) | 20 | 0.714 | 1.483 | 0.0154 | 1 |
| Retinoic acid receptors mediated signaling (PID) | 15 | 0.694 | 1.417 | 0.0358 | 0.7638 |
| IGF signaling (INOH) | 22 | 0.673 | 1.433 | 0.0219 | 0.6932 |
| Regulation of RAS family activation (PID) | 21 | 0.665 | 1.405 | 0.0379 | 0.7746 |
| FGF signaling pathway (PID) | 23 | 0.663 | 1.408 | 0.0351 | 0.8159 |
| GPCRs other (WikiPathways) | 35 | 0.634 | 1.445 | 0.0199 | 0.7079 |
| Human thyroid stimulating hormone signaling pathway (WikiPathways) | 39 | 0.632 | 1.459 | 0.011 | 0.8781 |
| Signaling by FGFR (Reactome) | 35 | 0.597 | 1.366 | 0.0382 | 0.7321 |
| Fibroblast growth factor 1 (NetPath) | 40 | 0.593 | 1.383 | 0.0427 | 0.754 |
| MAPK signaling pathway (WikiPathways) | 73 | 0.547 | 1.33 | 0.0427 | 0.7644 |
| Signaling by GPCR (Reactome) | 457 | 0.446 | 1.164 | 0.034 | 0.8706 |
| Metabolism | |||||
| Superpathway of conversion of glucose to acetylCoA and entry into the TCA cycle (HumanCyc) | 15 | 0.711 | 1.418 | 0.0379 | 0.7746 |
| C21 steroid hormone biosynthesis and metabolism (EHMN) | 25 | 0.664 | 1.449 | 0.0186 | 0.8017 |
| Androgen and estrogen biosynthesis and metabolism (EHMN) | 39 | 0.663 | 1.54 | 0.0033 | 1 |
| Central carbon metabolism in cancer (KEGG) | 33 | 0.652 | 1.46 | 0.009 | 0.9084 |
| Metabolism of nucleotides (Reactome) | 29 | 0.646 | 1.443 | 0.0174 | 0.7035 |
| Selenocysteine synthesis (Reactome) | 41 | 0.623 | 1.448 | 0.0154 | 0.7547 |
| Glycerophospholipid metabolism (KEGG) | 36 | 0.608 | 1.372 | 0.0446 | 0.75 |
| Pi metabolism (Reactome) | 31 | 0.605 | 1.378 | 0.0382 | 0.7201 |
| Biological oxidations (Reactome) | 82 | 0.576 | 1.399 | 0.0093 | 0.7397 |
| Purine metabolism (KEGG) | 62 | 0.562 | 1.355 | 0.0295 | 0.7328 |
| Phospholipid metabolism (Reactome) | 83 | 0.551 | 1.359 | 0.0115 | 0.7141 |
| Metabolism of carbohydrates (Reactome) | 119 | 0.532 | 1.338 | 0.0192 | 0.7502 |
| Metabolism of amino acids and derivatives (Reactome) | 143 | 0.507 | 1.294 | 0.0193 | 0.8099 |
Gene set enrichment analysis was performed with differentially methylated genes and gene sets from ConsensusPathDB. Gene set names and their source database (shown in parenthesis) with nominal P value lower than 0.05 are listed. FDR q values were presented. PID, pathway interaction database; INOH, integrating network objects with hierarchies; EHMN, Edinburgh