Table 1.
Genomic features of Differentially Methylated Regions (DMRs) in colon cancer
| N | # CpG | Genomic size | Median size (bp) | Overlap with islands | Overlap with shores | Overlap with Ref seq mRNA TSS | |
|---|---|---|---|---|---|---|---|
| Normal genome (reference) | N/A | 28.2M | 3.10 Gb | N/A | 27.7K | 55.4K | 36,983 |
| Hypomethylated blocks | 13,540 | 16.2M | 1.95 Gb | 39,412 | 17.6% | 26.8% | 10,453 |
| Hypermethylated blocks | 2,871 | 485K | 35.8 Mb | 9,213 | 13.4% | 36.4% | 976 |
| Hypomethylated small DMRs | 4,315 | 59.5K | 2.91 Mb | 401 | 2.2% | 51.0% | 1,708 |
| Novel hypomethylated | 448 | 8.35K | 367 Kb | 658 | 2.9% | 19.9% | 30 |
| Shift of methylation boundary | 1,516 | 17.5K | 741 Kb | 261 | 2.1% | 92.8% | 1,313 |
| Other | 2,351 | 33.7K | 1.80MB | 479 | 2.1% | 29.9% | 368 |
| Hypermethylated small DMRs | 5,810 | 403K | 6.14 Mb | 820 | 67.2% | 17.0% | 3,068 |
| Loss of boundary* | 1,756 | 165K | 2.36 Mb | 1,159 | 80.9% | 3.4% | 1,091 |
| Shift of methylation boundary | 1,774 | 96.3K | 1.40 Mb | 502 | 60.3% | 33.0% | 1,027 |
| Other | 2,280 | 142K | 2.38MB | 769 | 62.2% | 15.1% | 983 |
*
As described in the text, loss of boundary DMRs were associated with increase of methylation in the CpG island and a decrease of methylation in the adjacent shore. We score these as a single event and classify them here since there are more CpGs in the islands than in the shores.