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Table 6 Canonical pathways associated with genes whose expression levels correlate with the level of DNA methylation in nonagenarians

From: Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression

Ingenuity canonical pathways p-value (B-H corrected) Ratio Molecules
Integrin signalling 0.016 0.054 ITGB1,PTK2,RAP2A,FYN,PAK1,RALA,ACTA2,ITGA6,CAPN2,ITGAL,ACTN1
Actin cytoskeleton signalling 0.017 0.048 ITGB1,PTK2,TIAM1,PAK1,F2R,ACTA2,TRIO,PDGFD,GSN,ARHGAP24,ACTN1
Tec kinase signalling 0.019 0.051 STAT4,ITGB1,PTK2,FYN,GNAI3,GNB4,PAK1,ACTA2,HCK
Agrin interactions at neuromuscular junction 0.019 0.090 ITGB1,PTK2,PAK1,ACTA2,ITGA6,ITGAL
Paxillin signalling 0.020 0.064 ITGB1,PTK2,PAK1,ACTA2,ITGA6,ITGAL,ACTN1
Reelin signalling in neurons 0.026 0.073 ITGB1,FYN,HCK,ITGA6,ARHGEF11,ITGAL
Phospholipase C signalling 0.030 0.041 ITGB1,FYN,GNB4,RALA,AHNAK,SYK,MEF2C,ARHGEF11,PLD6,CREB5
Germ cell-sertoli cell junction signalling 0.030 0.051 ITGB1,PTK2,TGFBR2,PAK1,ACTA2,ITGA6,GSN,ACTN1
Crosstalk between dendritic cells and natural killer cells 0.030 0.066 IFNG,ACTA2,CD86,HLA-F,ITGAL,CCR7
Protein kinase A signalling 0.030 0.035 TGFBR2,PTK2,GNB4,GNAI3,TCF4,PTPN7,YWHAG,DUSP10,RYR1,LEF1,CREB5,PTPRM,SIRPA
Antigen presentation pathway 0.030 0.100 PSMB9,IFNG,HLA-F,HLA-DPB1
Fcγ receptor-mediated phagocytosis in macrophages and monocytes 0.030 0.063 FYN,PAK1,SYK,ACTA2,HCK,PLD6
T helper cell differentiation 0.037 0.073 STAT4,TGFBR2,IFNG,IFNGR2,CD86
Ephrin receptor signalling 0.038 0.041 ITGB1,PTK2,FYN,GNAI3,GNB4,PAK1,PDGFD,CREB5
Caveolar-mediated endocytosis signalling 0.044 0.062 ITGB1,FYN,ACTA2,ITGA6,ITGAL
  1. Canonical pathways (IPA [34]) associated with genes whose expression levels correlate with the level of DNA methylation. P-values are Benjamini-Hochberg corrected. Ratio = number of identified genes/number of genes in the pathway. Molecules refer to genes affected in our analysis present in the given pathway.