Table 5.
Neurological functions enriched among DAGs implicated by CpGs within 500 bp from the TSS in the mild subgroup.
| Nervous System Development & Function | p-Value * | DAGs (<500 bp from TSS) |
|---|---|---|
| Mild subtype | Hypermethylated | |
| Development of striatum | 1.26 × 10−6 | ARX, CNTNAP2, GSX1, PAX6 |
| Abnormal morphology of nervous system | 3.61 × 10−6 | ARX, ATP8A2, CDH11, CNTNAP2, EDN3, FOXB1, FST, GSX1, OSTM1, PAX6, RBP1, SYN2, TFAP2A, TLX3, ZIC1 |
| Abnormal morphology of glutamatergic neuron | 4.96 × 10−5 | PAX6,TLX3 |
| Migration of neurons | 5.84 × 10−5 | ARX, CNTNAP2, ERRFI1, FLRT2, LRP12, PAX6, TLX3 |
| Development of neurons | 9.20 × 10−5 | ARX, ATP8A2, CADM1, CCN1, CDH1, CNTNAP2, FLRT2, ITGA1, LRP12, PAX6, SYN2, TLX3, TPBG |
| Quantity of neurons | 1.19 × 10−4 | ARX, CADM1, CNTNAP2, ENTPD3, FST, PAX6, PTGER2, SYN2, TFAP2A |
| Abnormal morphology of brain | 1.23 × 10−4 | ARX, CNTNAP2, FOXB1, GSX1, OSTM1, PAX6, SYN2, TFAP2A, ZIC1 |
| Abnormal morphology of forebrain | 1.94 × 10−4 | ARX, CNTNAP2, FOXB1, GSX1, PAX6, TFAP2A |
| Growth of cerebellum | 2.30 × 10−4 | FOXB1, ZIC1 |
| Cell cycle progression of neurons | 9.71 × 10−4 | PAX6, ZIC1 |
| Growth of brain | 1.22 × 10−3 | ARX, FOXB1, PAX6, ZIC1 |
| Developmental process of synapse | 1.83 × 10−3 | CADM1, CDH1,FLRT2, SYN2, TPBG |
| Initiation of migration of neurons | 2.90 × 10−3 | ARX |
| Formation of forebrain | 3.02 × 10−3 | ARX, CNTNAP2, GSX1, PAX6, ZIC1 |
| Synaptic transmission of hippocampal CA1 region | 4.14 × 10−3 | CNTNAP2, SYN2 |
| Development of sensory neurons | 4.39 × 10−3 | PAX6, TLX3 |
| Association of synaptic vesicles | 5.80 × 10−3 | SYN2 |
| Mild subtype | Hypomethylated | |
| Sensory system development | 6.57 × 10−9 | ABCA4, ADCY1, AIPL1, AIRE, ALDH1A2, ALOX15, APOB, AQP1, ARSG, ASPA, ATP2B2, BBS1, BBS7, BCL9L, BFSP2, BMPR1B, BRD1, C5AR1, CABP4, CCL1, CDH5, CDK20, CNGA3, COL18A1, COL1A1, COL8A2, CPLX4, CRX, CRYAA/CRYAA2, CRYAB, CRYBA4, CRYBB2, CRYGA, CRYGB, CRYGC, CXCR3, DNMT3A, DPT, DSC1, EGFR, ELOVL4, EMX1, FABP7, FASLG, FEZF2, FGF1, FGF7, FGFR2, FYCO1, GDF3, GFRA1, GJA3, GNAT2, GRK1, GUCA1A, GUCY2F, HCN1, HGF, HK2, HRG, IL1R1, IRX3, KERA, KNG1, KRT12, KRT4, LCK, LCTL, LHX2, LRAT, LRP8, LYVE1, MARCKSL1, METRN, MFAP2, MFRP, MGAT5, MSX2, NEUROD2, NEUROD4, NOTCH3, NRTN, NTF3, NTF4, NXNL1, OLIG2, OPN4, PDCD1, PDE6B, PDE6C, PF4V1, PLA2G3, POR, POU4F2, POU4F3, PPT2, PRPH2, PTGS2, PTPRS, PYGO1, RB1, RBP3, RDH8, RHO, RPE65, RUNX3, S1PR3, SERPINF1, SIX3, SIX6, SLC17A8, SLC39A5, SOX10, SOX11, SPI1, TFB1M, TH, THBS1, TP63, TRPV4, TUB, TULP1, TYRP1, USH2A, VCAM1, VSX2, WNT2 |
| Activation of neuroglia | 1.35 × 10−8 | ABCA4, ADIPOQ, AGT, ALB, C1QA, C5AR1, CCL1, CCL11, CCL21, CCL22, CCL5, CCL7, CD40LG, CHGA, CNGA3, CSF3, DRD2, EGFR, F2, FASLG, FGA, FGF1, FGG, GFAP, GJB1, GJC2, GRK2, IL10, IL1R1, MC4R, MOG, MSTN, MYOD1, NOS3, NR4A1, NRG1, PDE6B, PDK4, PTGS2, RDH8, SERPINF2, SLC6A4, SST, TLR7, TLR9, TREM2, TRPM2, VTN |
* Fisher exact p-value indicating the probability that the function is not enriched among the DAGs for this subgroup.