mCSEA

mCSEA is an R package designed to address the challenge of identifying differentially methylated regions (DMRs) in epigenetic analysis, particularly when subtle but consistent methylation changes are associated with complex disorders. While many existing methods focus on detecting significant differences in methylation levels, mCSEA is specifically tailored to detect these moderate yet consistent changes in DNA methylation.
This tool implements a Gene Set Enrichment Analysis method and is compatible with data generated from Illumina450K and EPIC arrays. It also offers the capability to integrate gene expression data and discover genes exhibiting significant correlations between methylation and gene expression patterns. Comparative evaluations using simulated datasets demonstrate that mCSEA outperforms other tools in the detection of DMRs.
In an application to real data involving sibling pairs with intrauterine hyperglycemia exposure, mCSEA successfully identifies differentially methylated promoters in genes associated with metabolic disorders like obesity and diabetes, highlighting its potential to uncover DMRs that may remain undetected by other methods.