Cited by 364Fungal and yeast genetics researchBioinformatics and Genomic NetworksGene Regulatory Network Analysis

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

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Baryshnikova, Anastasia, Costanzo, Michael, Kim, Yungil, Ding, Huiming, Koh, Judice, Toufighi, Kiana, Youn, Ji-Young, Ou, Jiongwen +11 more·2010·Nature Methods

Abstract

Global quantitative analysis of genetic interactions is a powerful approach for deciphering the roles of genes and mapping functional relationships among pathways. Using colony size as a proxy for fitness, we developed a method for measuring fitness-based genetic interactions from high-density arrays of yeast double mutants generated by synthetic genetic array (SGA) analysis. We identified several experimental sources of systematic variation and developed normalization strategies to obtain accurate single- and double-mutant fitness measurements, which rival the accuracy of other high-resolution studies. We applied the SGA score to examine the relationship between physical and genetic interaction networks, and we found that positive genetic interactions connect across functionally distinct protein complexes revealing a network of genetic suppression among loss-of-function alleles.

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Authors
Baryshnikova, A., Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J.-Y., Ou, J., San Luis, B.-J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A.-C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., & Myers, C. L.
Affiliations
  • University of Toronto (CA)
  • University of Minnesota (US)
  • Jackson Laboratory (US)
  • Santa Clara University (US)
  • Mount Sinai Hospital (CA)
  • Princeton University (US)
Corresponding author
  • Andrews, Brenda
  • Boone, Charles
  • Myers, Chad L
Venue
Nature Methods
Published
2010-11-14
Volume
7
Issue
12
Pages
1017-1024
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W1967220526
Cited by
364
References
41
Citations by year
2026: 10 · 2025: 16 · 2024: 19 · 2023: 15 · 2022: 20 · 2021: 23 · 2020: 26 · 2019: 18 · 2018: 26 · 2017: 38 · 2016: 29 · 2015: 15 · 2014: 26 · 2013: 40 · 2012: 21
FWCI
10.81
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
Funders
  • Canadian Institutes of Health Research (MOP79368, GSP-415-67)
  • National Human Genome Research Institute (R01HG005084)
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 › Gene Regulatory Network Analysis
Keywords
synthetic genetic array, genetic interactions, fitness measurement, double mutants, yeast, colony size, normalization, genetic suppression, protein complexes, loss-of-function alleles
MeSH terms
Algorithms, Mutation, Ultraviolet Rays, Yeasts, Gene Expression Regulation, Fungal, Mutagenesis, Genome, Fungal, Oligonucleotide Array Sequence Analysis, Genome-Wide Association Study, Genetic Fitness

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