MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E. Garrett-Bakelman, Maria Figueroa, Ari Melnick, Christopher E. Mason

Research output: Contribution to journalArticle

400 Citations (Scopus)

Abstract

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, thatrapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation andhydroxymethylation sequencing experiments. methylKit includes functions for clustering, samplequality visualization, differential methylation analysis and annotation features, thus automatingand simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statisticallysignificant regions of differential methylation and stratify tumor subtypes. methylKit is availableat http://code.google.com/p/methylkit.

Original languageEnglish (US)
Article numberR87
JournalGenome Biology
Volume13
Issue number10
DOIs
StatePublished - Oct 3 2012
Externally publishedYes

Fingerprint

methylation
DNA methylation
DNA Methylation
Methylation
genome
cytosine
Cytosine
Genome
DNA
cancer
neoplasms
Epigenomics
epigenetics
breast neoplasms
Cluster Analysis
Neoplasms
tumor
Breast Neoplasms
visualization
Genes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F. E., Figueroa, M., Melnick, A., & Mason, C. E. (2012). MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biology, 13(10), [R87]. https://doi.org/10.1186/gb-2012-13-10-R87

MethylKit : a comprehensive R package for the analysis of genome-wide DNA methylation profiles. / Akalin, Altuna; Kormaksson, Matthias; Li, Sheng; Garrett-Bakelman, Francine E.; Figueroa, Maria; Melnick, Ari; Mason, Christopher E.

In: Genome Biology, Vol. 13, No. 10, R87, 03.10.2012.

Research output: Contribution to journalArticle

Akalin, A, Kormaksson, M, Li, S, Garrett-Bakelman, FE, Figueroa, M, Melnick, A & Mason, CE 2012, 'MethylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles', Genome Biology, vol. 13, no. 10, R87. https://doi.org/10.1186/gb-2012-13-10-R87
Akalin, Altuna ; Kormaksson, Matthias ; Li, Sheng ; Garrett-Bakelman, Francine E. ; Figueroa, Maria ; Melnick, Ari ; Mason, Christopher E. / MethylKit : a comprehensive R package for the analysis of genome-wide DNA methylation profiles. In: Genome Biology. 2012 ; Vol. 13, No. 10.
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