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Table 5 Canonical pathways associated with reproducible DEGs with Alu insertion predicted by the Ingenuity Pathway Analysis (IPA)

From: Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder

Ingenuity canonical pathways Benjamini-Hochberg P value Gene symbol
ILK signaling 6.39E−08 PPP2R5E, GSK3B, CDC42, PTEN, IRS2, CREB1, PIK3R4, RHOQ, PIK3R1, MYH9, PIK3CG, PTPN11, MAP2K4, ITGB1, MAPK1, CREBBP, LIMS1, FNBP1, NACA
Neurotrophin/TRK signaling 3.20E−07 CDC42, MAP3K5, IRS2, CREB1, PTPN11, MAP2K4, PIK3R4, MAPK1, CREBBP, PIK3R1, SHC1, PIK3CG
NGF signaling 5.11E−07 CDC42, MAP3K5, IRS2, CREB1, PIK3R4, SMPD1, PIK3R1, PIK3CG, PTPN11, MAP2K4, TRIO, MAPK1, CREBBP, SHC1
Reelin signaling in neurons 1.02E−06 GSK3B, ITGAL, IRS2, FYN, PTPN11, MAP2K4, ITGB1, PIK3R4, PIK3R1, YES1, LYN, PIK3CG
HGF signaling 1.24E−06 CDC42, MAP3K5, IRS2, PIK3R4, ELF2, PIK3R1, PIK3CG, PTPN11, MAP2K4, ITGB1, MAPK1, ETS1, HGF
ERK/MAPK signaling 2.73E−06 PPP2R5E, PAK2, IRS2, CREB1, PIK3R4, ELF2, PRKAG2, PIK3R1, PIK3CG, FYN, PTPN11, ITGB1, MAPK1, CREBBP, ETS1, SHC1
Insulin receptor signaling 5.09E−06 GSK3B, PTEN, IRS2, PIK3R4, PRKAG2, RHOQ, PIK3R1, CBL, PIK3CG, FYN, PTPN11, MAPK1, SHC1
Axonal guidance signaling 2.47E−05 SEMA4D, GSK3B, CDC42, PAK2, IRS2, PIK3R4, PLXNC1, GNB1, PPP3CB, PRKAG2, ADAM10, PIK3R1, RASSF5, PIK3CG, GNAI2, FYN, PPP3R1, PTPN11, ITGB1, MAPK1, PLCL2, SHC1
IL-6 signaling 4.05E−05 ABCB1, MAP4K4, IRS2, PTPN11, MAP2K4, PIK3R4, MAPK1, PIK3R1, SHC1, IL6ST, PIK3CG
Neuroinflammation signaling pathway 4.51E−05 GSK3B, IRS2, CREB1, PIK3R4, PPP3CB, PIK3R1, TBK1, PIK3CG, CFLAR, PPP3R1, PTPN11, MAP2K4, MAPK1, CREBBP, CYBB, TLR2, NFE2L2
Glucocorticoid receptor signaling 4.78E−05 IRS2, CREB1, NCOA1, PIK3R4, SMARCA2, PPP3CB, PRKAG2, PIK3R1, PIK3CG, TAF4, PPP3R1, PTPN11, MAP2K4, HSPA5, MAPK1, CREBBP, ARID1A, SHC1
PI3K/AKT signaling 1.22E−04 PPP2R5E, GSK3B, MAP3K5, PTEN, ITGB1, MAPK1, LIMS1, PIK3R1, SHC1, PIK3CG
CREB signaling in neurons 1.49E−04 IRS2, CREB1, PIK3R4, GNB1, PRKAG2, PIK3R1, PIK3CG, GNAI2, PTPN11, MAPK1, CREBBP, PLCL2, SHC1
Synaptic long-term potentiation 6.29E−03 PPP3R1, CREB1, PPP3CB, MAPK1, CREBBP, PRKAG2, PLCL2
Estrogen receptor signaling 9.05E−03 TAF4, NCOA1, CTBP2, MAPK1, CREBBP, TRRAP, SHC1
Androgen signaling 1.19E−02 GNAI2, NCOA1, GNB1, MAPK1, CREBBP, PRKAG2, SHC1
  1. Canonical pathways are significantly associated with 320 overlapping genes that were identified in multiple studies. P values calculated by Fisher’s exact test with Benjamini-Hochberg correction (FDR = 0.05) for each function are shown