ArticleNucleic acids research2013
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- DiffMethylTools: a toolbox for the detection, annotation, and visualization of differential methylation.Life science alliance · 2026Article
- Nonparametric Bayes Differential Analysis of Multigroup DNA Methylation Data.Bayesian analysis · 2025Article
- Article
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- HBCR_DMR: A Hybrid Method Based on Beta-Binomial Bayesian Hierarchical Model and Combination of Ranking Method to Detect Differential Methylation Regions in Bisulfite Sequencing Data.Journal of personalized medicine · 2024Article
- A novel approach toward optimal workflow selection for DNA methylation biomarker discovery.BMC bioinformatics · 2024Article
- A novel family of beta mixture models for the differential analysis of DNA methylation data: An application to prostate cancer.PloS one · 2024Article
- Differential methylation region detection via an array-adaptive normalized kernel-weighted model.PloS one · 2024Article
- Article
- Transgenerational Epigenetic DNA Methylation Editing and Human Disease.Biomolecules · 2023Review
- EpiMix is an integrative tool for epigenomic subtyping using DNA methylation.Cell reports methods · 2023Article
- EpiMix: an integrative tool for epigenomic subtyping using DNA methylation.bioRxiv : the preprint server for biology · 2023Article
- Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis.Journal of computational biology : a journal of computational molecular cell biology · 2022Review
- Pancreatoblastomas and mixed and pure acinar cell carcinomas share epigenetic signatures distinct from other neoplasms of the pancreas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- WGCNA-Based DNA Methylation Profiling Analysis on Allopurinol-Induced Severe Cutaneous Adverse Reactions: A DNA Methylation Signature for Predisposing Drug Hypersensitivity.Journal of personalized medicine · 2022Article
- Epigenetic study of early breast cancer (EBC) based on DNA methylation and gene integration analysis.Scientific reports · 2022Article
- Air pollution-induced epigenetic changes: disease development and a possible link with hypersensitivity pneumonitis.Environmental science and pollution research international · 2021Review
- Follistatin supplementation induces changes in CDX2 CpG methylation and improves in vitro development of bovine SCNT preimplantation embryos.Reproductive biology and endocrinology : RB&E · 2021Article
- Clinical epigenomics for cardiovascular disease: Diagnostics and therapies.Journal of molecular and cellular cardiology · 2021Review
- Comprehensive analysis of gene expression and DNA methylation for preeclampsia progression.Journal of the Chinese Medical Association : JCMA · 2021Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
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/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.