Unlock your biological data
In addition to the single CpG analysis, a second approach can be used to perform differential methylation analysis to bring further confidence in the results. It consists in looking at regional methylation measurements rather than at single site measurements, and therefore in identifying differentially methylated regions rather than DMPs (Hansen et al., 2011; Hansen et al., 2012). The principle of this method resides in the fact that probes being close together (e.g. inside the promoter of the same gene or in a window of a given size) should have the same behavior, i.e. hypomethylated (or hypermethylated) in the cases as compared with control samples.
(Hansen et al., 2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet.
(Hansen et al., 2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol.
(Dedeurwaerder et al., 2014) A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform.