Genome-wide analysis of CpG methylation in human CD34⁺ cells compared with CD34⁻ cells. The log₂ intensity ratio of CpG methylation (CD34⁺/CD34⁻) was averaged from 4 experiments. (A) The mean intensity ratio of probes is shown in 100-bp–sized windows up to 3 kb upstream and downstream of the TSS of known genes; error bar represents 95% CI. Negative log₂ ratio values are indicative of a relative undermethylation around the TSS (−150 bp to 300 bp of the TSS) in CD34⁺ cells compared with CD34⁻ cells. In flanking regions, positive log₂ ratio values are indicative of a relative overmethylation in this region, up to 3 kb of upstream and downstream of the TSS, in CD34⁺ cells. (B) Genome-wide plot of the number of genes with respect to mean log₂ ratios for 3 regions around the TSS (−150 bp to 300 bp, −1.5 kb to −150 bp, and 300 bp to 1.5 kb of the TSS). The log₂ distribution encompassing the TSS (−150 bp to 300 bp) exhibits a normal-shaped curve with a peak markedly shifted toward negative direction, indicating an undermethylation in this region in CD34⁺ cells compared with CD34⁻ cells. (C) Separate analysis of log₂ intensity ratios for CGI⁺ and CGI⁻ gene clusters. Log₂ ratios for probes for CpG islands (CGI⁺) and non-CpG islands (CGI⁻) were separately plotted with respect to distance from the TSS. Both CGI⁺ and CGI⁻ genes exhibit an undermethylation dip around the TSS in CD34⁺ cells compared with CD34⁻ cells and CGI⁻ genes are hypermethylated in the flanking regions. (D) A log2 distribution plot of CGI⁺ and CGI⁻ genes shows the TSS flanking regions of CGI⁻ genes are skewed toward positive values, indicating hypermethylation.