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Cited by 128Evolution and Genetic DynamicsGenomics and Phylogenetic StudiesBioinformatics and Genomic Networks

The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

Open access
Chen, Jenny, Swofford, Ross, Johnson, Jeremy, Cummings, Beryl B., Rogel, Noga, Lindblad-Toh, Kerstin, Haerty, Wilfried, Palma, Federica di, Regev, Aviv·2019·Genome Research
DOI 10.1101/gr.237636.118PMC PMC6314168

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Abstract

The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene's expression, parameterize the distribution of each gene's optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.

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  1. 10.2307/2346101 · DOI
  2. 10.2307/2411186 · DOI

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Metadata

Authors
Chen, J., Swofford, R., Johnson, J., Cummings, B. B., Rogel, N., Lindblad-Toh, K., Haerty, W., Palma, F. D., & Regev, A.
Affiliations
  • Broad Institute (US)
  • Earlham Institute (GB)
  • University of East Anglia (GB)
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2018-12-14
Volume
29
Issue
1
Pages
53-63
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.237636.118
PMC
PMC6314168
OpenAlex
W2949594216
Cited by
128
References
66
Citations by year
2026: 18 · 2025: 18 · 2024: 18 · 2023: 14 · 2022: 13 · 2021: 24 · 2020: 16 · 2019: 5 · 2018: 2
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • UEA Digital Repository (University of East Anglia) (acceptedVersion)
  • Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • Broad Institute
  • Vetenskapsrådet
  • National Institutes of Health (5rm1hg006193-10)
  • Klarman Cell Observatory, Broad Institute
  • Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR9817, BBS/E/T/000PR5885, BBS/E/T/000PR9818, BB/CSP1720/1)
  • National Human Genome Research Institute (RM1‐HG006193, T32HG002295)
  • National Institute of Neurological Disorders and Stroke
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
gene expression evolution, Ornstein-Uhlenbeck process, stabilizing selection, directional selection, neutral selection, comparative transcriptomics, mammals
MeSH terms
Animals, Dogs, Gene Expression Regulation, Models, Genetic, Rabbits, Evolution, Molecular

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