methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
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DOI：
10.1186/gb-2012-13-10-r87
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发表时间：
2012-10-03
期刊：
影响因子：
12.3
通讯作者：
Mason CE
中科院分区：
文献类型：
--
作者：
Akalin A;Kormaksson M;Li S;Garrett-Bakelman FE;Figueroa ME;Melnick A;Mason CE
DNA甲基化是胞嘧啶碱基的化学修饰，对于基因调控、细胞特化和癌症发展至关重要。在这里，我们描述了一个R软件包，甲基试剂盒，快速分析全基因组胞嘧啶表观遗传图谱的高通量甲基化和羟甲基化测序实验。methylKit包括聚类、样品质量可视化、差异甲基化分析和注释功能，从而自动化和简化了识别DNA甲基化的统计学显著碱基或区域的许多步骤。最后，我们展示了乳腺癌数据上的甲基化试剂盒，在其中我们发现了差异甲基化的统计学显著区域，并对肿瘤亚型进行了分层。methylKit可在http://code.google.com/p/methylkit上获得。
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.
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