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/ webcite); 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.

van Eijk et al.

van Eijk et al. BMC Genomics 2012 13:636   doi:10.1186/1471-2164-13-636

Open Data