Supplementary Data 1 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition

Supplemental Data 1. This spreadsheet contains the results of the differential methylation analysis, the meta-analysis and the pathway analysis. In the meta-analysis sheets, the first 3 columns represent the chromosomal locations, followed by the significance level (stat, p-value, and FDR). Weight.1 and weight.2 represent the weight of early and late data respectively. For the meta-analysis we weighted both as 1. The effect size represents the difference in DNA methylation between NP and P at the early and late time points (effect size.1=early, effect size.2=late), and the p-value for each is next depicted. We then filtered the data by trimmed means as in the Materials and Methods section and the new values are listed in columns N and O. We then annotated the gene name, which genomic feature the loci resides in, and the distance to the nearest promoter (distance to feature). We then annotated the mean coverage and the number of CpG sites in the differentially methylated region. The differential methylation sheets include similar data without the columns pertaining to the meta-analysis. The 3Ingenuity Pathway Analysis (IPA) spreadsheets contain the pathway analysis result. The pathway name, followed by the statistical significance, and molecules represented in our data for each pathway are detailed on each sheet. The analysis was first conducted on the hyper and hypomethylated genes separately, then the combined hyper and hypermethylated genes were analyzed together.