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. Author manuscript; available in PMC: 2014 Nov 1.
Published in final edited form as: Nat Neurosci. 2013 Nov 24;17(1):121–130. doi: 10.1038/nn.3588

Figure 2.

Figure 2

Changes in DNA methylation are concordant within a differentially methylated region. (a) Plot of DNA methylation for individual CpGs within a hypermethylated DMR in intron 1 of NDRG1. Above the plot is the complete gene structure, with dotted lines indicating the zoomed region containing the DMR shown in the plot. Methylation for individual multiple sclerosis cases and controls is plotted in red and black, respectively, with red and black lines connecting the mean methylation for each consecutive CpG assayed. (b) Plot of hypomethylated CpGs in intron 2 of LRRC27. Plot as described in a. Arrowheads indicate CpGs that were assayed in c. (c) Methylation for individual CpGs assessed using MassARRAY EpiTYPER. Plots are as shown in a. Below the plot is the local DNA sequence surrounding each CpG. Arrowheads indicate CpGs with corresponding Illumina probes in b. (d) Pearson’s correlation between methylation measured by the Illumina array and Sequenom assay (n = 39 DNA brain samples). Plot shows data for the CpG with the highest cross-platform correlation; however, all CpGs tested showed correlation coefficients r > 0.6. (e) Summary of Pearson’s correlations of CpG methylation at sites measured by both Illumina array and Sequenom assays.