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COHCAP MIRA / 450k Comparison [450k]

ABSTRACT: Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP) Keywords: HES-2

ORGANISM(S): Homo sapiens

SUBMITTER: Charles Warden

PROVIDER: E-GEOD-42707 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Warden Charles D CD Lee Heehyoung H Tompkins Joshua D JD Li Xiaojin X Wang Charles C Riggs Arthur D AD Yu Hua H Jove Richard R Yuan Yate-Ching YC

Nucleic acids research 20130417 11

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 r ...[more]

PMID: 23598999

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COHCAP MIRA / 450k Comparison [MIRA]

Project description:Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP) Keywords: HES-2

2013-06-08 | E-GEOD-42734 | biostudies-arrayexpress

COHCAP: City of Hope CpG Island Analysis Pipeline

Project description:COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data. It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. COHCAP is currently the only DNA methylation package that can handle integration with gene expression data, and the results of this study show that COHCAP can identify regions of differential methylation with ~50% concordance with gene expression. COHCAP is scalable for analysis of both cell line data and heterogeneous patient data, and it can identify known cancer biomarkers as well as intriguing new roles of epigenetic regulation in cancer (such as methylation of estrogen receptor in breast cancer patients). This study also uses cell line data to show that COHCAP is capable of analyzing Illumina methylation array and targeted bisulfite sequencing data, with either 1-group or 2-group study designs. The accuracy of COHCAP is accessed using qPCR, EpiTect, and comparison of COHCAP regions of differential methylation with MIRA peaks. This software is freely available at https://sourceforge.net/projects/cohcap/. The following third-party datasets were utilized in the paper: BS-Seq data: GSE26826 Additional Microarray Data: GSE29290 This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-06-08 | E-GEOD-42310 | biostudies-arrayexpress

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Project description:Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen

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COHCAP HCT116 Mutant Comparison [methylation]

Project description:Genome-wide expression and methylation differences are compared for a normal HCT116 cell line and a derived mutant with altered DNA methylation patterns. The data compares the effect of a gene mutation on genome-wide expression (and methylation). This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP) Keywords: parental, mutant

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