Methylation levels of 32 DMRs in promoters that decreased following GEN exposure.

GEN, genistein; DMR, differentially methylated region.Position: GEN-mediated DMRs were identified by MspI fragment-based DNA methylation typing; these DMRs contain more than two consecutive probes with log2 (HpaIIr/McrBCr) values unidirectionally different between the control and GEN-treated samples; the difference is greater than mean ± 3SD (Figure S6). Positions of each DMR in the mouse genome assembly, February 2006, NCBI36/mm8, are shown.Gene(s): the names of the gene(s) adjacent to the DMR are given. In some cases, a DMR contained two distinct, bi-directional promoters.Control and GEN: the mean and standard deviation of the log2 (HpaIIr/McrBCr) values for all probes within the DMR. Data were sorted from high to low for the Control log2 (HpaIIr/McrBCr) data.DM/T: the ratio of the number of differentially methylated (DM) probes (the difference is greater than mean ± 3SD) to the total (T) number of probes within a DMR.Class: promoter classification based on the CpG density. High CpG-density promoters (HCPs) contain at least one 500-bp region with GC content >0.55 and have a ratio of observed to expected CpGs >0.6. Low CpG-density promoters (LCPs) lack the 500-bp GC-rich interval and the ratio of observed to expected CpGs is >0.4. Intermediate CpG-density promoters (ICPs) have characteristics between HCPs and LCPs.Ref.: the methylation levels of the various types of tissues of the corresponding region in human genome. Methylation levels of Methylated (M), Intermediately methylated (I), and Unmethylated (U) derive from the Ensembl genome-wide DNA methylation resource (E-TABM-445). ND denotes a lack of available information about the methylation level of the human counterpart.*This DMR integrated two proximate probes that were similarly hypomethylated following GEN treatment; one probe resided in the MspI interval of chr14:101869393–101869526, and the other was in chr14:101869523–101869657.