title: COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.
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/.
authors.affiliation: Bioinformatics Core, City of Hope National Medical Center, Duarte, CA 91010, USA. cwarden@coh.org
authors.forename: Charles D
authors.initials: CD
authors.lastname: Warden
authors.forename: Heehyoung
authors.initials: H
authors.lastname: Lee
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Tompkins
authors.forename: Xiaojin
authors.initials: X
authors.lastname: Li
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
authors.forename: Arthur D
authors.initials: AD
authors.lastname: Riggs
authors.forename: Hua
authors.initials: H
authors.lastname: Yu
authors.forename: Richard
authors.initials: R
authors.lastname: Jove
authors.forename: Yate-Ching
authors.initials: YC
authors.lastname: Yuan
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D015870:Gene Expression; D023281:Genomics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite