TitlemethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Publication TypeJournal Article
Year of Publication2012
AuthorsAkalin, Altuna, Kormaksson Matthias, Li Sheng, Garrett-Bakelman Francine E., Figueroa Maria E., Melnick Ari, and Mason Christopher E.
JournalGenome Biol
Date Published2012 Oct 03
KeywordsBreast Neoplasms, Cell Line, Tumor, DNA Methylation, Epigenesis, Genetic, Female, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, MCF-7 Cells, Sequence Analysis, DNA, Software

<p>DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit.</p>

Alternate JournalGenome Biol
PubMed ID23034086
PubMed Central IDPMC3491415
Grant ListP30 AG013283 / AG / NIA NIH HHS / United States
R01 NS076465 / NS / NINDS NIH HHS / United States
/ WT_ / Wellcome Trust / United Kingdom
1R01NS076465-01 / NS / NINDS NIH HHS / United States