Table 2.
Distribution of results over CpG islands and shores
| Location | Illumina Human Methylation 27 | Methylation & expression cis | Methylation & expression trans | Methylation & expression & SNP cis | ||||
|---|---|---|---|---|---|---|---|---|
|
Island |
11,582 |
42% |
70 |
13.5%,
p
<2.2e-16↓ |
269 |
38.2%, p=0.04 |
11 |
15.1%,
p
=1.1e-06↓ |
|
Island shore (2kb) |
8,718 |
32% |
184 |
35.6%, p=0.056 |
172 |
24.4%,
p
=3.9e-05↓ |
39 |
53.4%,
p
=1.3e-04↑ |
|
Outside island/shore |
7,278 |
26% |
263 |
50.9%,
p
<2.2e-16↑ |
264 |
37.4%,
p
=2.5e-10↑ |
23 |
31.5%, ns |
| Total | 27,578 | 517 | 705 | 73 | ||||
Methylation probes were classified into three categories according to UCSC browser ( http://genome.ucsc.edu/); CpG islands, CGI shores (up to 2kb around an island) and outside islands or shores. Differences compared to Illumina Human Methylation 27K array were tested using Fisher’s Exact for count data (Bonferroni threshold p:0.05/9=0.006). A downward arrow indicates significantly lower percentage of probes while an upward arrow indicates significantly higher percentage of observations compared to the overall probe distribution on the Illumina array.