Evidence map›Paper›PMID 39093129›Full record

ArticleEpigenomics2024

An assessment of compositional methods for the analysis of DNA methylation-based deconvolution estimates.

Alexander Alsup, Emily Nissen, Lucas A Salas, Annette M Molinaro, Alexander Reiner, Simin Liu, Tracy E Madsen, Longjian Liu, Paul L Auer, Brock C Christensen and 3 more

Abstract read
In one paragraph

Article in Epigenomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

13 authors.

Alexander AlsupDepartment of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA.ORCID 0000-0002-9487-4686
Emily NissenDepartment of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA.ORCID 0000-0001-9020-336X
Lucas A SalasDepartment of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA.ORCID 0000-0002-2279-4097
Annette M MolinaroDepartment of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.
Alexander ReinerDivision of Public Health Science, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.ORCID 0000-0002-0607-6714
Simin LiuDepartment of Emergency Medicine, Alpert Medical School of Brown University and Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI 02903, USA.ORCID 0000-0003-2098-3844
Tracy E MadsenDepartment of Emergency Medicine, Alpert Medical School of Brown University and Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI 02903, USA.
Longjian LiuDepartment of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA.
Paul L AuerDivision of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
Brock C ChristensenDepartment of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA.ORCID 0000-0003-3022-426X
John K WienckeDepartment of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0001-7101-6489
Karl T KelseyDepartment of Emergency Medicine, Alpert Medical School of Brown University and Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI 02903, USA.ORCID 0000-0002-2302-1600
Devin C KoestlerDepartment of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA.ORCID 0000-0002-0598-0146

Funding

Mentoring CoreP20GM103418 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI Douglas E Wright · 2012 to 2026
$63.0M
Transgenic & Gene-Targeting Shared ResourceP30CA168524 · NCI · UNIVERSITY OF KANSAS MEDICAL CENTER · PI ROY A. JENSEN · 2012 to 2026
$40.1M
Using Integrated Omics to Identify Dysfunctional Genetic Mechanisms Influencing Schizophrenia and Sleep DisturbancesP20GM130423 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI Kalyani Pyaram, Steven Allan Soper · 2019 to 2026
$21.5M
NCI NIH HHS P30 CA168524NIGMS NIH HHS P20 GM103418NIGMS NIH HHS P20 GM130423
6 · The paper itself

Abstract

DNA methylation (DNAm)-based deconvolution estimates contain relative data, forming a composition, that standard methods (testing directly on cell proportions) are ill-suited to handle. In this study we examined the performance of an alternative method, analysis of compositions of microbiomes (ANCOM), for the analysis of DNAm-based deconvolution estimates. We performed two different simulation studies comparing ANCOM to a standard approach (two sample

Indexed as

DNA MethylationComputer SimulationFemaleHumansMicrobiotaANCOMcell proportion datacompositional datadeconvolutionWomen’s Health Initiative

Identifiers

PMID39093129
PMCPMC11418214

What OpenQuestion holds

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Registered trials

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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.