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

TLDR

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification, and cancer development. The authors present methylKit, an R package that rapidly analyzes genome‑wide cytosine epigenetic profiles from high‑throughput methylation and hydroxymethylation sequencing experiments. methylKit automates and simplifies key steps—including clustering, sample quality visualization, differential methylation analysis, and annotation—to identify statistically significant methylated bases or regions. Applied to breast‑cancer data, the package identifies statistically significant differential methylation regions and enables stratification of tumor subtypes. methylKit is available at http://code.google.com/p/methylkit.

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, 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.