Table 4.
Neurological functions and diseases enriched among DAGs implicated by CpGs within 500 bp of the TSS in the intermediate subgroup.
| Nervous System Development & Function | p-Value * | DAGs (<500 bp from TSS) |
| Intermediate subtype | Hypermethylated | |
| Loss of neurites | 4.64 × 10−4 | CORT, GJB1, NTF3, SERPINA3 |
| Activation of neuroglia | 1.11 × 10−3 | C1QA, CCL11, CCL22, FGF1, GJB1, NOS3, SMPD3 |
| Abnormal morphology of neurons | 1.22 × 10−3 | ATP2B2, C1QA, CABP4, CCL11, CORT, GJB1, KCNQ1, NOS3, NTF3, OPN4, PAX8, PLP1, RHO, SERPINA3, SORBS2 |
| Abnormal morphology of nerve ending | 1.66 × 10−3 | C1QA, NTF3 |
| Abnormal morphology of sensory neurons | 2.16 × 10−3 | ATP2B2, KCNQ1, NTF3, OPN4, PAX8 |
| Loss of axons | 2.38 × 10−3 | CORT, GJB1, NTF3 |
| Activation of astrocytes | 3.04 × 10−3 | C1QA, CCL11, FGF1, SMPD3 |
| Formation of excitatory synapses | 3.22 × 10−3 | NTF3, SORBS2 |
| Abnormal morphology of neurites | 5.98 × 10−3 | CORT, GJB1, NTF3, PLP1, SERPINA3, SORBS2 |
| Evoked potential | 6.24 × 10−3 | ATP2B2, KCNQ1, NTF3, PAX8 |
| Abnormal morphology of nervous system | 6.49 × 10−3 | ATP2B2, C1QA, CABP4, CCL11, CNGA2, CORT, FGF1, GJB1, KCNQ1, NOS3, NR5A1, NTF3, OPN4, PAX8, PLP1, RHO, SERPINA3, SMPD3, SORBS2 |
| Intermediate subtype | Hypomethylated | |
| Morphology of brain | 8.83 × 10−4 | ARSA, CTNNB1, GBX2, GSX1, TFAP2A |
| Differentiation of sensory progenitor cells | 9.40 × 10−4 | CTNNB1 |
| Neurogenesis of dopaminergic neurons | 1.88 × 10−3 | CTNNB1 |
| Abnormal morphology of forebrain | 2.42 × 10−3 | ARSA, GSX1, TFAP2A |
| Abnormal morphology of brain | 3.12 × 10−3 | ARSA, GBX2, GSX1, TFAP2A |
| Auditory evoked potential | 3.15 × 10−3 | ARSA, KCNQ1 |
| Cell survival of dopaminergic neurons | 3.76 × 10−3 | CTNNB1 |
| Formation of forebrain | 3.77 × 10−3 | CTNNB1, GBX2, GSX1 |
| Accumulation of microglia | 7.50 × 10−3 | CTNNB1 |
| Lack of cerebellum | 8.43 × 10−3 | GBX2 |
| Neurological Diseases | p-Value * | DAGs (<500 bp from TSS) |
| Intermediate subtype | Hypermethylated | |
| Abnormal morphology of mechanosensory neurons | 8.56 × 10−4 | ATP2B2, KCNQ1, NTF3, PAX8 |
| Lack of muscle sensory neurons | 7.85 × 10−3 | NTF3 |
| Intermediate subtype | Hypomethylated | |
| Early-onset neurological disorder | 3.20 × 10−4 | ARSA, GABRA3, KCNQ1, PDZRN3 |
| Cognitive impairment | 3.54 × 10−4 | ARSA, CTNNB1, GABRA3, GSTM1, KCNQ1, TFAP2A |
| Autosomal dominant mental retardation type 19 | 9.40 × 10−4 | CTNNB1 |
| Early-onset schizophrenia | 1.13 × 10−3 | GABRA3, PDZRN3 |
| Lack of cerebellum | 8.43 × 10−3 | GBX2 |
* Fisher exact p-value indicating the probability that the function or disorder is not enriched among the DAGs for this subgroup.