Figure 3. Genomic context of CpG methylation.

A schematic diagram of CpGs (A) depicts their genomic context relative to the nearest CpG island (top) or gene (bottom). Island context was defined similarly to the Illumina manifest (see material and methods) as being within an “island” (brown), in a 4kb “shore” flanking the island (yellow), or in an “open sea” more than 4kb from an island. Gene context was defined relative to the nearest open reading frame being: within 1500 (TSS1500; purple) or 200 bp (TSS200; pink) of a transcription start site; in the 5′UTR (green), the 1^st exon of a transcript (green); in the body of gene (orange) or the 3′UTR (red). Pie charts (B) show the distribution of the CpGs examined based upon their genomic context for all probes retained from the array (top), for all the probes identified as differentially methylated between OSIS- and EIUM- (middle), and for all the differentially methylated probes that were matched to differentially expressed transcripts (bottom; note that stacked bar graphs show the CpG island context broken down for each of the gene contexts.).