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COCOA: coordinate covariation analysis of epigenetic heterogeneity.

ABSTRACT: A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA's utility by analyzing DNA methylation, ATAC-seq, and multi-omic data in supervised and unsupervised analyses, showing that COCOA provides new understanding of inter-sample epigenetic variation. COCOA is available on Bioconductor ( http://bioconductor.org/packages/COCOA ).

SUBMITTER: Lawson JT

PROVIDER: S-EPMC7487606 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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COCOA: coordinate covariation analysis of epigenetic heterogeneity.

Lawson John T JT Smith Jason P JP Bekiranov Stefan S Garrett-Bakelman Francine E FE Sheffield Nathan C NC

Genome biology 20200907 1

A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses covariation of epigenetic signals across individuals and a database of region sets to annotate epigenetic heterogeneity. COCOA is the first such tool for DNA methylation data and can also analyze any epigenetic signal with genomic coordinates. We demonstrate COCOA's utility by analyzing DNA me ...[more]

PMID: 32894181

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