Evidence map›Paper›PMID 37537644›Full record

ArticleGenome biology2023

BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures.

Saba Ghaffari, Kelly J Bouchonville, Ehsan Saleh, Remington E Schmidt, Steven M Offer, Saurabh Sinha

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

Article in Genome biology, 2023. 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
0.8field-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, 5 citations in OpenAlex.

  1. Integration of Bulk and Single-Cell RNA Sequencing Analyses in Biomedicine.International journal of molecular sciences · 2026
    Review
  2. Review
  3. Article
  4. bioRxiv : the preprint server for biology · 2023
    Article
  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

6 authors at 3 institutions in 1 country.

Saba GhaffariDepartment of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA.ORCID http://orcid.org/0000-0003-0791-3905
Kelly J BouchonvilleDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA.
Ehsan SalehDepartment of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA.
Remington E SchmidtDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA.
Steven M OfferDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA. Offer.Steven1@mayo.edu.
Saurabh SinhaWallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, Georgia Institute of Technology, 3108 U.A. Whitaker Bldg., 313 Ferst Drive, Atlanta, GA, 30332, USA. saurabh.sinha@bme.gatech.edu.
Mayo Clinic · USUniversity of Illinois Urbana-Champaign · USGeorgia Institute of Technology · US

Funding

High-content microscopy platform for multiplex perturbation/multiplex readout studiesR35GM130119 · NIGMS · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Traver Hart · 2018 to 2026
$3.9M
A precision medicine approach to improve prediction of severe toxicity in fluorouracil chemotherapy (Diversity Supplement)R01CA251065 · NCI · UNIVERSITY OF IOWA · PI Steven Offer · 2021 to 2026
$2.1M
Quantitative Regulatory Genomics: Networks, CIS-Regulatorycodes, and Phenotypic VariationR35GM131819 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI SINHA, SAURABH · 2019 to 2023
$1.8M
NCI NIH HHS R01 CA251065NIGMS NIH HHS R35 GM130119NIGMS NIH HHS R35 GM131819
6 · The paper itself

Abstract

Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help differentiate these scenarios. BEDwARS is a Bayesian deconvolution method designed to address differences between reference signatures of cell types and corresponding true signatures underlying bulk transcriptomic profiles. BEDwARS is more robust to noisy reference signatures and outperforms leading in-class methods for estimating cell type proportions and signatures. Application of BEDwARS to dihydropyridine dehydrogenase deficiency identified the possible involvement of ciliopathy and impaired translational control in the etiology of the disorder.

Indexed as

Gene Expression ProfilingTranscriptomeBayes TheoremBayesian inferenceBulk gene expression deconvolutionDihydropyridine dehydrogenase deficiencySingle cell RNA-seq

Identifiers

PMID37537644
PMCPMC10399072
OpenAlexW4385553317

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.