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Table 4 Diseases and biological functions 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

Disease or function annotation Benjamini-Hochberg P value No. of genes Gene symbol
Autism or intellectual disability 2.19E−04 21 ABCB1, ADNP, ANKRD11, ARID1A, ATP6V1A, CAMTA1, CASP2, CDC42, CHD4, COL4A3BP, CREBBP, GNB1, OPA1, PTEN, SLC35A3, SMARCA2, SON, TRIO, UBE3A, YY1, ZMYND11
Neuromuscular disease 5.70E−04 34 ABCB1, ADAM10, ALCAM, ANKRD11, ATP2A2, ATP6V1A, ATXN1, CANX, CASP2, CFLAR, GSK3B, HBP1, HMGCR, HSPA5, IFNAR2, IL7R, KIF1B, LDLR, MAP2K4, MBP, MBTPS1, NOTCH2, OSBPL8, PPP3CB, PTPRC, PTPRE, RUNX3, SSX2IP, TLR2, TOMM20, TRIO, USP13, WNK1, XRCC6
Synthesis of reactive oxygen species 7.52E−04 14 CANX, CDC42, CYBB, ETS1, FCER1A, HGF, ITGB1, MAP2K4, MAPK1, PIK3CG, PTEN, SHC1, TLR2, TXNRD1
Disorder of basal ganglia 9.21E−04 29 ABCB1, ANKRD11, ATP2A2, ATP6V1A, ATXN1, CA2, CASP2, CFLAR, GSK3B, HBP1, HMGCR, HSPA5, KIF1B, LDLR, MAP2K4, MBP, MBTPS1, NOTCH2, OSBPL8, PTPRE, RUNX3, SAMHD1, SSX2IP, TOMM20, TRIO, USP13, WNK1, XPR1, XRCC6
Dyskinesia 9.44E−04 23 ABCB1, ANKRD11, ATP2A2, ATP6V1A, ATXN1, CASP2, CFLAR, HBP1, HMGCR, HSPA5, LDLR, MAP2K4, MBTPS1, NOTCH2, OSBPL8, PTPRE, RUNX3, SSX2IP, TOMM20, TRIO, USP13, WNK1, XRCC6
Mental retardation 1.13E−03 18 ADNP, ANKRD11, ARID1A, ATP6V1A, CAMTA1, CASP2, CDC42, CHD4, COL4A3BP, CREBBP, GNB1, OPA1, SLC35A3, SMARCA2, SON, TRIO, YY1, ZMYND11
Brain lesion 1.36E−03 33 ANKRD11, ANXA7, APC, ARCN1, ARID1A, ATP6V1A, CA2, CBL, CREBBP, CTBP2, DICER1, DOCK5, EHD4, HGF, HMGCR, IRS2, LDLR, LYST, NCOA1, NF1, PABPC1, PIK3R1, PRKCSH, PTEN, PTPN11, SAP130, SON, TBK1, TOP1, TRIM33, TRIP11, TRRAP, ZCCHC6
Cognitive impairment 1.44E−03 20 ADNP, ANKRD11, ARID1A, ATP6V1A, CA2, CAMTA1, CASP2, CDC42, CHD4, COL4A3BP, CREBBP, GNB1, HMGCR, OPA1, SLC35A3, SMARCA2, SON, TRIO, YY1, ZMYND11
Dementia 1.62E−03 27 ADAM10, APLP2, ATXN1, CA2, CANX, CASP2, DICER1, GSK3B, HMGCR, HSPA5, LDLR, LIMS1, NFE2L2, OPA1, PIK3R1, PTEN, PTPRE, RUNX3, SLC6A6, SMPD1, SPG21, SRPK2, TBK1, TFCP2, TRIO, UBQLN1, WDR7
  1. Neurological diseases and functions 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) and the number of genes for each function are shown