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

Autor: Ghaffari S; Department of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA., Bouchonville KJ; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA., Saleh E; Department of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA., Schmidt RE; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA., Offer SM; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA. Offer.Steven1@mayo.edu., Sinha S; Wallace 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.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2023 Aug 03; Vol. 24 (1), pp. 178. Date of Electronic Publication: 2023 Aug 03.
DOI: 10.1186/s13059-023-03007-7
Abstrakt: 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.
(© 2023. BioMed Central Ltd., part of Springer Nature.)
Databáze: MEDLINE
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