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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.