The effect of CpG methylation is likely to extend beyond the core of promoter regions (Mikkelsen et al., 2007, Weber et al., 2007), and core promoter regions from 500 bp upstream and 200 bp downstream of the transcription start site were also analyzed. A summarized methylation level was calculated for each gene based on the average signal intensity of all the probes within the gene's regulatory region, from -1,300 bp to +500 bp (Average level analysis). We considered promoters with DNA methylation levels higher than 1.3-fold of the genome-wide median methylation level as hypermethylated promoters. This threshold is similar to that used in the MeDIP-chip analysis of human fibroblast. Promoters with DNA methylation levels lower than 1.3-fold of the genome-wide median methylation level were considered hypomethylated (Weber et al., 2007).
