COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis

被引：98

作者：

Warden, Charles D. ^{[1
,2
]}

Lee, Heehyoung ^{[3
]}

Tompkins, Joshua D. ^{[4
,5
]}

Li, Xiaojin ^{[6
,7
]}

Wang, Charles ^{[6
,7
]}

Riggs, Arthur D. ^{[4
,5
]}

Yu, Hua ^{[3
]}

Jove, Richard ^{[2
]}

Yuan, Yate-Ching ^{[1
,2
]}

机构：

[1] City Hope Natl Med Ctr, Bioinformat Core, Duarte, CA 91010 USA

[2] City Hope Natl Med Ctr, Dept Mol Med, Duarte, CA 91010 USA

[3] City Hope Natl Med Ctr, Canc Immunotherapeut & Immunol, Duarte, CA 91010 USA

[4] City Hope Natl Med Ctr, Dept Biol, Duarte, CA 91010 USA

[5] City Hope Natl Med Ctr, Dept Diabet & Metab Dis Res, Duarte, CA 91010 USA

[6] City Hope Natl Med Ctr, Funct Genom Core, Duarte, CA 91010 USA

[7] City Hope Natl Med Ctr, Dept Mol & Cellular Biol, Duarte, CA 91010 USA

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / 11期

基金：

美国国家卫生研究院;

关键词：

EPIGENOME-WIDE ASSOCIATION; CLINICAL-SAMPLES; BREAST-CANCER; CPG SITES; EXPRESSION; MICROARRAY; ARRAY; GENES; NORMALIZATION; VALIDATION;

D O I：

10.1093/nar/gkt242

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing. The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites. COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with similar to 50% concordance with gene expression from both cell line data and heterogeneous patient data. For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression. COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression. This software is freely available at ext-link-type="uri" xlink:href="https://sourceforge.net/projects/cohcap/" xmlns:xlink="http://www.w3.org/1999/xlink">https://sourceforge.net/projects/cohcap/.

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