Cited by 454Genetics, Aging, and Longevity in Model OrganismsGenomics and Phylogenetic StudiesGene expression and cancer classification

Comparing genomic expression patterns across species identifies shared transcriptional profile in aging

McCarroll, Steven A, Murphy, Coleen T, Zou, Sige, Pletcher, Scott D, Chin, Chen-Shan, Jan, Yuh Nung, Kenyon, Cynthia, Bargmann, Cornelia I +1 more·2004·Nature Genetics

Abstract

We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation.

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Crossref · 10.1038/ng1291

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  • GBA approaches are widely used to identify new potential disease genes if a substantial proportion of the genes within a module are associated with a particular disease.

    “GBA approaches are also widely used to identify new potential disease genes if a substantial proportion of the genes within a module are associated with a particular disease [26, 121–126] (Figure 1).”
  • Deregulation of mitochondrial function is a common feature across multiple aspects of aging.

    “Deregulation of mitochondrial function is a common feature in multiple aspects of aging.”

    From PGC-1α in aging and anti-aging interventions (2009) · cites this paper as [6]

  • The cited findings suggest mitochondrial dysfunction has a causal role in aging and mitochondrial adaptation is central to CR's retardation of aging.

    “Taken together these findings suggest of a causal role of mitochondrial dysfunction in the aging process and a central role for mitochondrial adaptation in the mechanism of aging retardation by CR”

    From PGC-1α in aging and anti-aging interventions (2009) · cites this paper as [6]

  • Genes involved in mitochondrial energy metabolism are among the key pathways universally regulated with aging.

    “Foremost among these and pertinent to this review are genes involved in mitochondrial energy metabolism.”

    From PGC-1α in aging and anti-aging interventions (2009) · cites this paper as [6]

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Authors
McCarroll, S. A., Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C.-S., Jan, Y. N., Kenyon, C., Bargmann, C. I., & Li, H.
Affiliations
  • University of California, San Francisco (US)
  • University College London (GB)
  • Howard Hughes Medical Institute (US)
Corresponding author
Li, Hao
Venue
Nature Genetics
Published
2004-01-18
Volume
36
Issue
2
Pages
197-204
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
OpenAlex
W2118852675
Cited by
454
References
51
Citations by year
2026: 1 · 2025: 7 · 2024: 6 · 2023: 9 · 2022: 8 · 2021: 28 · 2020: 15 · 2019: 13 · 2018: 15 · 2017: 15 · 2016: 16 · 2015: 15 · 2014: 17 · 2013: 12 · 2012: 29
FWCI
14.46
Type
journal article
Language
en
Open access
closed
Locations
  • Nature Genetics (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Howard Hughes Medical Institute
  • Consorzio Interuniversitario Biotecnologie
  • National Institute on Deafness and Other Communication Disorders
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Keywords
gene expression comparison, orthologs, aging, gene expression signatures, Gene Ontology, Caenorhabditis elegans, Drosophila melanogaster, mitochondrial metabolism, DNA repair, larval development, embryonic development, gametogenesis, mRNA degradation
MeSH terms
Age Factors, Aging, Animals, Drosophila melanogaster, Gene Expression Regulation, Humans, Phylogeny, Saccharomyces cerevisiae, Time Factors, Caenorhabditis elegans, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Databases, Genetic

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