Table 3.
Neurological functions and diseases enriched among DAGs implicated by CpGs within 500 bp of the TSS in the severely language-impaired subgroup.
| Nervous System Development & Function | p-Value * | DAGs (<500 bp from TSS) |
| Severely language-impaired subtype | Hypermethylated | |
| Cell-cell adhesion of neurons | 2.29 × 10−4 | CADM1, NINJ2 |
| Induction of neural crest | 2.37 × 10−3 | TFAP2A |
| Scaffolding of postsynaptic region | 3.55 × 10−3 | CADM1 |
| Corticogenesis | 3.55 × 10−3 | PAX6 |
| Quantity of neurons | 7.25 × 10−3 | CADM1, NPTX2, PAX6, TFAP2A |
| Abnormal morphology of brain | 7.37 × 10−3 | CRMP1, EPB41L1, PAX6, TFAP2A |
| Size of growth cone | 1.65 × 10−2 | PAX6 |
| Morphology of nervous system | 3.71 × 10−2 | CADM1, CRMP1, EPB41L1, PAX6, TFAP2A |
| Memory consolidation | 3.73 × 10−2 | PAX6 |
| Quantity of nerve ending | 3.73 × 10−2 | CADM1 |
| Development of sensory neurons | 3.95 × 10−2 | PAX6 |
| Abnormal morphology of forebrain | 4.58 × 10−2 | PAX6, TFAP2A |
| Severely language-impaired subtype | Hypomethylated | |
| Abnormal morphology of sensory neurons | 6.21 × 10−4 | ATP2B2, CETN2, KCNQ1, OPN4, PAX8 |
| Delay in initiation of maturation of interneurons | 5.93 × 10−3 | FMR1 |
| Abnormal morphology of neurons | 6.49 × 10−3 | ATP2B2, CABP4, CCL11, CETN2, CORT, FMR1, KCNQ1, NOS3, OPN4, PAX8, SHANK1 |
| Long term synaptic depression of hippocampal cells | 9.57 × 10−3 | FMR1, INS |
| Circadian phase shifting | 1.18 × 10−2 | OPN4 |
| Remodeling of dendrites | 1.18 × 10−2 | FMR1 |
| Density of GABAergic synapse | 1.18 × 10−2 | FMR1 |
| Neurological Diseases | p-Value * | DAGs (<500 bp from TSS) |
| Severely language-impaired subtype | Hypermethylated | |
| Autosomal dominant mental retardation type 11 | 1.19 × 10−3 | EPB41L1 |
| Cognitive impairment | 1.33 × 10−3 | CRMP1, EPB41L1, GSTM1, NPTX2, PAX6, TFAP2A |
| Epileptic seizure | 3.70 × 10−2 | CCN1, NPTX2 |
| Mental retardation | 4.09 × 10−2 | EPB41L1, PAX6, TFAP2A |
| Abnormal morphology of forebrain | 4.58 × 10−2 | PAX6, TFAP2A |
| Severely language impaired subtype | Hypomethylated | |
| Syndromic X-linked mental retardation | 2.20 × 10−5 | BCAP31, FMR1, PHF8, SLC1A7, SLC9A6, UBE2A |
| Cognitive impairment | 1.65 × 10−3 | BCAP31, FMR1, GRM4, INS, KCNQ1, LRRN4, NOS3, PDZK1, PHF8, POLR3C, SHANK1, SLC1A7, SLC9A6, UBE2A, UHMK1 |
| Fragile X-associated tremor ataxia syndrome | 5.93 × 10−3 | FMR1 |
| Fragile X syndrome with Prader-Willi-like phenotype | 5.93 × 10−3 | FMR1 |
| Movement Disorders | 1.15 × 10−2 | ATP2B2, ATP2B3, BCAP31, C9, CCL11, CETN2, COL6A3, F8A1, FCGR3A/FCGR3B, FMR1, KCNQ1, MYH7, OPN4, SDC4, SGCG, SLC17A4, SLC1A7, SLC9A6, TGM6 |
* Fisher exact p-value indicating the probability that the function or disorder is not enriched among the DAGs for this subgroup.