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Series GSE42310 Query DataSets for GSE42310
Status Public on Jun 08, 2013
Title COHCAP: City of Hope CpG Island Analysis Pipeline
Organism Homo sapiens
Experiment type Expression profiling by array
Methylation profiling by genome tiling array
Summary 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

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.
Overall design Refer to individual Series.
Citation(s) 23598999
Submission date Nov 15, 2012
Last update date Mar 27, 2019
Contact name Charles David Warden
Organization name City of Hope
Department Department of Molecular and Cellular Biology
Street address 1500 East Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platforms (3)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL16353 NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array (100718_HG18_CpG_Refseq_Prom_MeDIP)
Samples (14)
GSM1037504 parental1 [expression]
GSM1037505 parental2 [expression]
GSM1037506 parental3 [expression]
This SuperSeries is composed of the following SubSeries:
GSE42307 COHCAP HCT116 Mutant Comparison [expression]
GSE42308 COHCAP HCT116 Mutant Comparison [methylation]
GSE42707 COHCAP MIRA / 450k Comparison [450k]
BioProject PRJNA181146

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE42310_RAW.tar 350.9 Mb (http)(custom) TAR (of CEL, IDAT, PAIR)

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