Evidence map›Paper›PMID 32894181›Full record

ArticleGenome biology2020

COCOA: coordinate covariation analysis of epigenetic heterogeneity.

John T Lawson, Jason P Smith, Stefan Bekiranov, Francine E Garrett-Bakelman, Nathan C Sheffield

Open access · goldAbstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.9field-weighted citation impact, top 27% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 12 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 3 institutions in 1 country.

John T LawsonDepartment of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Jason P SmithCenter for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
Stefan BekiranovCenter for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
Francine E Garrett-BakelmanDepartment of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
Nathan C SheffieldDepartment of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. nsheffield@virginia.edu.ORCID 0000-0001-5643-4068
University of Virginia · USUniversity of Virginia Cancer CenterUniversity of Virginia Health System · US

Funding

Training in Cell and Molecular BiologyT32GM139787 · NIGMS · UNIVERSITY OF VIRGINIA · PI Bryce Paschal · 2021 to 2026
$2.5M
A modular data analysis ecosystem using portable encapsulated projectsR35GM128636 · NIGMS · UNIVERSITY OF VIRGINIA · PI SHEFFIELD, NATHAN · 2018 to 2022
$1.9M
Transdisciplinary Big Data Science Training at UVaT32LM012416 · NLM · UNIVERSITY OF VIRGINIA · PI BROWN, DONALD E, LOUGHRAN, THOMAS P. · 2016 to 2020
$1.3M
National Institute of General Medical Sciences (US) GM128636NIGMS NIH HHS R35 GM128636NIGMS NIH HHS T32 GM139787NLM NIH HHS T32 LM012416
6 · The paper itself

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 ).

Indexed as

Epigenesis, GeneticGenetic HeterogeneitySoftwareBreast NeoplasmsDNA MethylationEpigenomicsHumansMolecular Sequence AnnotationCancerChromatin accessibilityData integrationDimensionality reductionDNA methylationEpigeneticsEZH2Multi-omicsPrincipal component analysis

Identifiers

PMID32894181
PMCPMC7487606
OpenAlexW3083309117

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.