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Table 2 Gene set enrichment analysis details are reported for DPMs (hypo- and hypermethylated genes) and DMRs

From: Genome-wide DNA methylation analysis in blood cells from patients with Werner syndrome

  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
  1. 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)