Table 2. Genomic features of CpGs and enrichment in conserved sites.
| Full set (850K) |
Conserved set (13665) |
||||
|---|---|---|---|---|---|
| Feature | Counts | Percent Total |
Counts | Percent Total |
Enrichment p3 |
| Gene features1 | |||||
| TSS1500 | 107193 | 12 | 1195 | 9 | ns |
| TSS200 | 65152 | 8 | 1940 | 14 | <1.0E-15 |
| 5'UTR | 73070 | 8 | 1269 | 9 | 1.8E-04 |
| 1stExon | 26433 | 3 | 2028 | 15 | <1.0E-15 |
| Exon | 5680 | 1 | 282 | 2 | <1.0E-15 |
| 3'UTR | 21594 | 2 | 340 | 2 | ns |
| Body | 318165 | 37 | 4918 | 36 | ns |
| Non-Genic | 249549 | 29 | 1693 | 12 | ns |
| CpG islands and flanking regions2 | |||||
| Islands | 161598 | 19 | 6270 | 46 | <1.0E-15 |
| Shores | 154735 | 18 | 2267 | 17 | ns |
| Shelves | 61811 | 7 | 664 | 5 | ns |
| Open Sea | 488692 | 56 | 4464 | 33 | ns |
1 CpG position relative to gene features based on annotations from Illumina (UCSC_RefGene_Group). TSS1500 and TSS200 are CpGs at –200 or 200–1500 upstream of are transcription start sites; Non-genic are CpG with no annotated gene features.
2 Shores = 0–2 kb from islands; shelves = 2–4 kb from islands
3 Enrichment of gene features and CpG regions in the conserved set compared to the full set based on hypergeometric test