Table 2.
Gene set enrichment analysis details are reported for DPMs (hypo- and hypermethylated genes) and DMRs
| Enriched pathways | Pathway ID | Overlap | P value | Combined score | Overlapping genes | |
|---|---|---|---|---|---|---|
| Hypermethylated probes | Glycosphingolipid biosynthesis | HSA-00603 | 3/14 | 0.001 | 2.29 | ST3GAL1, GBGT1, ST3GAL2 |
| FoxO signal pathway | HSA-04068 | 8/133 | 0.003 | 2.60 | MAPK10, USP7, AKT2, STAT3, PTEN, FOXO3, SKP2, GABARAP | |
| Insulin signalling pathway | HSA-04910 | 8/139 | 0.004 | 2.49 | MAPK10, PTPN1, SHC2, AKT2, PRKAK1B, FASN, TSC2, CRKL | |
| Hypomethylated probes | PI3K-Akt signalling | HSA_04151 | 16/341 | 0.006 | 3.46 | CSF-1R, CDKN1B, TNXB, VWF, LAMA1, FLT4, THBS1, PTK2, LPAR5, PPP2R2B, PPP2R2D, MAPK1, COL6A6, FGFR1, BCL2L1, ITGA9 |
| Focal adhesion | HSA_04510 | 12/202 | 0.01 | 3.26 | MAPK10, TNXB, VWF, ROCK2, LAMA1, FLT4, PXN, MAPK1, COL6A6, THBS1, PTK2, ITGA9 | |
| DMRs | Sphingolipid metabolism | HSA_00600 | 2/120 | 0.003 | 4.54 | CERS3, CERS1 |
| Sphingolipid signalling pathway | HSA_047071 | 1/47 | 0.001 | 5.36 | CERS3 |
Overlap indicates the number of hits from the differentially methylated gene sets compared to the KEGG gene set library, while “overlapping genes” column contains names of these hits. Differentially expressed genes between normal and WS fibroblasts in Cheung HH dataset [30] are reported. Enriched pathways were selected based on the P value. Combined score is a multiplication of the P value computed using Fisher’s exact test with the z-score of the deviation from the expected rank (see “Methods” for details)