Article ; Online: COCOA
Genome Biology, Vol 21, Iss 1, Pp 1-
coordinate covariation analysis of epigenetic heterogeneity
2020 Volume 23
Abstract: 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 ... ...
| Abstract | 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 ). |
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| Keywords | Epigenetics ; DNA methylation ; Chromatin accessibility ; Principal component analysis ; Dimensionality reduction ; Data integration ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470 |
| Language | English |
| Publishing date | 2020-09-01T00:00:00Z |
| Publisher | BMC |
| Document type | Article ; Online |
| Database | BASE - Bielefeld Academic Search Engine (life sciences selection) |
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