|
| 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 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.
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| |
|
| 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)
|
|
| 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] |
| GSE42734 |
COHCAP MIRA / 450k Comparison [MIRA] |
|
| Relations |
| BioProject |
PRJNA181146 |
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