Table 2. Number of differentially methylated probes between tumors and normal tissues in several subgroups of CRC at a false discovery rate of 0.05 (q-value<0.05).
| Data set |
HNPCC |
Sporadic CRCa |
CRCb | |||
|---|---|---|---|---|---|---|
| Subgroup | Overall | Lynch synd. | FCCTX | Overall | MSI-L/MSS | Overall |
| Samples | 36/40 | 19/20 | 10/11 | 194/32 | 171/25 | 129/29 |
| # Hypomethylation | 240 | 307 | 200 | 922 | 1,060 | 321 |
| In CGI (%) | 10 (4.2) | 9 (2.9) | 9 (4.5) | 96 (10.4) | 96 (9.1) | 11 (3.4) |
| In PR (%) | 212 (89.5) | 273 (89.5) | 176 (88.9) | 831 (91.5) | 961 (91.8) | 291 (91.5) |
| # Hypermethylation | 590 | 780 | 170 | 1,497 | 1,387 | 1,182 |
| In CGI (%) | 475 (80.5) | 591 (75.8) | 142 (83.5) | 1,039 (69.4) | 971 (70.0) | 874 (73.9) |
| In PR (%) | 520 (97.6) | 688 (96.5) | 151 (97.4) | 1,329 (96.4) | 1,230 (96.5) | 1,063 (97.3) |
CGI, CpG island; CRC, colorectal cancer; FCCTX, familial colorectal cancer type X; HNPCC, hereditary nonpolyposis colorectal cancer; MSI, microsatellite instability; MSS, microsatellite stable; PR, promoter region; TCGA, the cancer genome atlas.
Row 3 gives the number of tumors and normal tissues in each data set, with that for tumors placed in the front; row 4 reports the number of hypomethylated probes; row 5 lists the number (percentage) of hypomethylated probes located in CGIs; row 6 describes the number (percentage) of hypomethylated probes located in PRs, which are defined as being located within 1 kb upstream and 1 kb downstream from the transcription start site; rows 7–9 provide information that is similar to that given in rows 4–6, but for hypermethylated probes.
TCGA.