Why Are There Still Over 1000 Uncharacterized Yeast Genes?
Open accessAbstract
The yeast genetics community has embraced genomic biology, and there is a general understanding that obtaining a full encyclopedia of functions of the ∼6000 genes is a worthwhile goal. The yeast literature comprises over 40,000 research papers, and the number of yeast researchers exceeds the number of genes. There are mutated and tagged alleles for virtually every gene, and hundreds of high-throughput data sets and computational analyses have been described. Why, then, are there >1000 genes still listed as uncharacterized on the Saccharomyces Genome Database, 10 years after sequencing the genome of this powerful model organism? Examination of the currently uncharacterized gene set suggests that while some are small or newly discovered, the vast majority were evident from the initial genome sequence. Most are present in multiple genomics data sets, which may provide clues to function. In addition, roughly half contain recognizable protein domains, and many of these suggest specific metabolic activities. Notably, the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory.
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Scientific research tends to focus on well-studied proteins, leading to neglect of poorly understood genes.
“It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected.”
From Functional unknomics: Systematic screening of conserved genes of unknown function (2023) · cites this paper as [5]
The section “Do Uncharacterized Genes Have Any Distinguishing Characteristics in Large-Scale Analyses?” (p. 4) says uncharacterized yeast genes are studied less frequently, and “How Will We Complete the Encyclopedia of the Cell?” (p. 5) urges researchers to focus on them. The paper does not establish that research generally favors well-studied proteins or that the relative lack of attention is unjustified; it also considers biological reasons these genes may be difficult to characterize. (LLM, conf=0.83)
Experimental — accuracy not yet measuredResearch efforts continue to focus on genes and proteins of known function, with similar trends in gene and protein annotation databases.
“Analysis of publication trends has revealed that research efforts continue to focus on genes and proteins of known function, with similar trends seen in gene and protein annotation databases [2,4,5].”
From Functional unknomics: Systematic screening of conserved genes of unknown function (2023) · cites this paper as [5]
The section “Do Uncharacterized Genes Have Any Distinguishing Characteristics in Large-Scale Analyses?” (p. 4) says uncharacterized yeast genes are studied less frequently and are less represented in interaction databases. This supports the direction of the claim, but the paper does not establish the broader publication and annotation-database trends for genes and proteins generally. (LLM, conf=0.84)
Experimental — accuracy not yet measuredSome genes may have roles that are not relevant to laboratory conditions.
“Finally, some genes may have roles that are not relevant to laboratory conditions [5].”
From Functional unknomics: Systematic screening of conserved genes of unknown function (2023) · cites this paper as [5]
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References 63 · Cited by 161
- Authors
- Peña-Castillo, L., & Hughes, T. R.
- Affiliations
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- University of Toronto (CA)
- Corresponding author
- Hughes, Timothy R
- ORCID
- Hughes, Timothy R
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-01
- Volume
- 176
- Issue
- 1
- Pages
- 7-14
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC1893027
- OpenAlex
- W2120886934
- Cited by
- 161
- References
- 63
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 3 · 2023: 10 · 2022: 2 · 2020: 1 · 2019: 4 · 2018: 6 · 2017: 9 · 2016: 10 · 2015: 4 · 2014: 7 · 2013: 11 · 2012: 17
- FWCI
- 1.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- uncharacterized genes, Saccharomyces cerevisiae, gene function annotation, Saccharomyces Genome Database, protein domains, yeast metabolism, genome annotation
- MeSH terms
- Genes, Fungal, Yeasts, Open Reading Frames, Genome, Fungal, Genomics
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