Supplementary Table 4. Top 10nervous system-related gene functional categories that are significantly enriched in the top 200 ASD candidate genes from five published GWASs 1-5(Supplementary table 1) using Ingenuity pathway analysis ( . The genes encoding proteins that could be directly placed in one or more of the three networks involved in ASDs (Figures 1-3) are indicated in bold. The functional categories that are directly involved in neurite outgrowth or synaptic function are underlined.
Category / Genes / Significance a / Adjusted significance b
Neurological disease
(81/200 genes) / ABCC1,ACTN2,ADA,ADAMTS3,AKAP7,
APP,ATP1B1,ATXN2L,BAG5,C10ORF11,
CADPS,CDCA7,CNGA3,COLEC12,CRBN,
CRIM1,CTNNA2,CTNNA3,CUGBP2,
DAB1,DCC,DHRS3,DMD,DNER,DYNLT1,
FAM171A1,FGF1,FHIT,GALNT13,
GALNTL4,GANC,GDAP1,GDNF,GPR98,
GRIN2A,HRH2,IQGAP2,JARID2,KCNA1,
KCNB1,KLC1,LRP1B,MAML2,MARCKS,
MAST3,MEIS2,MYO5A,MYO5B,NDRG1,
NEFM,NGF,NID1,NPAS3,NTM,OR52I1,
OTX2,P2RY1,PIK3R1,PTPRE,PTPRN2,
RIMS1,SEMA4D,SEMA5A,SGCD,SGCZ,
SGEF,SHH,SIPA1L2,SKAP1,SORCS2,SOX2,SPATA16,SRGAP3,ST8SIA2,SUCLG2,
SYT17,SYTL3,THOC1, TMEM132D,
TOX, TSHZ1 / 9.79E-07 / 1.64E-04
Development of CNS / APP, CTNNA2, DAB1, FEZF2, JARID2, MARCKS, MYO5A, OTX2, SH3GL3, SHH, SIX3, SOX2, ST8SIA2, TLX1 / 8.03E-06 / 9.17E-04
Development of neurites / APP, DCC, DMD, FEZF2, GDNF, MSN, NGF, PTPRE, SHH, SLITRK5, THBS4 / 3.28E-05 / 3.29E-03
Shape change of neurites / APP, DCC, DYNLT1, GDNF, NGF / 3.44E-05 / 3.32E-03
Sprouting of neurites / APP, DYNLT1, GDNF, NGF / 7.63E-05 / 6.39E-03
Neurological process of axons / APP, DCC, FEZF2, GDNF, OTX2, PTPRE, SEMA5A, SHH / 1.33E-04 / 8.78E-03
Quantity of synaptic vesicles / APP, MYO5A, RIMS1 / 1.53E-04 / 9.87E-03
Growth of axons / APP,DCC,GDNF, NGF, PLXNA4, SEMA5A / 2.14E-04 / 1.31E-02
Neurogenesis / APP,CRIM1,DCC,FEZF2,FGF1,GDNF,
NGF,OTX2,PLXNA4,SEMA5A,SHH,SOX2, ST8SIA2, THBS4 / 8.32E-04 / 3.87E-02
Outgrowth of neurites / APP,DCC,FRK,GDNF,MARCKS,NGF,
PLXNA4,SEMA5A, SH2B1 / 8.56E-04 / 3.91E-02

Abbreviations: ASD(s), autism spectrum disorder(s); CNS, central nervous system; GWASs, genome-wide association studies

a Single test P value calculated with the right-tailed Fisher’s exact test and taking into consideration both the total number of

molecules from the analysed dataset and the total number ofmolecules that is linked to the same gene category according to

the Ingenuity Knowledge Base.

b Multiple test-corrected P values using the Benjamini-Hochberg correction; only categories with more than one gene are shown.

References

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