Methylation patterns of normal gastric tissue. (A) Chromosome-wide average MES is shown as a function of the average CpG density, gene density (the number of genes per Mb), LINE quantity (the length of LINE per Mb), and SINE quantity (the length of SINE per Mb) for each chromosome. (B) For chromosome 22, the average CpG density (shaded gray) and MES (black curve) were obtained in 1-Mb sliding windows. The positions of transcribed genes (black bars at the bottom), CG islands (blue bars at the top), and long repeats (> 1 kb; red bars on the top) are compared against the backdrop of DNA methylation and CpG density (left). The average MES for CGIs, gene bodies, and repeats (right). (C) The distribution of gene bodies and CGI MES (left). The average MES for promoter-associated and promoter-independent CGIs is shown to the right. (D) The average MES for promoter subgroups, based on the existence of CGI (left). (E) Basic information on intergenic, exonic, and intronic regions, according to length, CpG number, and mapped reads (left). The distribution of intergenic, exonic, and intronic MESs is shown to the right. (F) Basic information on the upstream 1-kb region, 5' UTR exons, coding exons, 3' UTR exons, and downstream 1-kb region according to length, CpG number, and mapped reads (left). The distribution of the MES for each element is shown to the right.
Park et al. BMC Medical Genomics 2011 4:82 doi:10.1186/1755-8794-4-82