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

Authors :
Warden CD
Lee H
Tompkins JD
Li X
Wang C
Riggs AD
Yu H
Jove R
Yuan YC
Source :
Nucleic acids research [Nucleic Acids Res] 2013 Jun; Vol. 41 (11), pp. e117. Date of Electronic Publication: 2013 Apr 17.
Publication Year :
2013

Abstract

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 ∼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 https://sourceforge.net/projects/cohcap/.

Details

Language :
English
ISSN :
1362-4962
Volume :
41
Issue :
11
Database :
MEDLINE
Journal :
Nucleic acids research
Publication Type :
Academic Journal
Accession number :
23598999
Full Text :
https://doi.org/10.1093/nar/gkt242