We further compared the DNA methylation patterns of the three promoter classes with gene expression levels (GEO Accession# GSE9545; Affymetrix microarray, n = 4) under the same treatment conditions and experimental settings. The majority of genes in the HCP promoter group were expressed (76.6% of the probe sets can be reliably detected as “present” in Affymetrix microarray by the MAS5 algorithm), followed by ICP (47.3% are “present”) and LCP (30.7%) (Chi-square p-value <2.2 × 10−16). In the ICP group, which contains a high methylation density, there was a clear inverse relationship between gene expression levels and promoter DNA methylation levels, measured by the average signal levels of all the probes in the promoter region (Fig. 3A; chi-square p-value <2.2 × 10−16). Microarray signals for 71% of the hypomethylated ICP promoters (methylation levels were at least 1.3-fold lower than the genome-wide median methylation level) were “present” in the gene expression microarray; in contrast, only 37% hypermethylated promoters were “present” (Fig. 3B; chi-square p-value <2.2 × 10−16).
