Cited by 2,162Bioinformatics and Genomic NetworksFungal and yeast genetics researchGene Regulatory Network Analysis

The Genetic Landscape of a Cell

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Costanzo, Michael, Baryshnikova, Anastasia, Bellay, Jeremy, Kim, Yungil, Spear, Eric D., Sevier, Carolyn S., Ding, Huiming, Koh, Judice L.Y. +45 more·2010·Science

Abstract

Making Connections: Genetic interaction profiles highlight cross-connections between bioprocesses, providing a global view of cellular pleiotropy, and enable the prediction of genetic network hubs. Costanzo et al. (p. 425 ) performed a pairwise fitness screen covering approximately one-third of all potential genetic interactions in yeast, examining 5.4 million gene-gene pairs and generating quantitative profiles for ∼75% of the genome. Of the pairwise interactions tested, about 3% of the genes investigated interact under the conditions tested. On the basis of these data, a reference map for the yeast genetic network was created.

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  • Synthetic genetic interaction screens in yeast show thousands of combinations of individually viable mutations can be jointly lethal, with similar examples in Drosophila and C. elegans.

    “Synthetic genetic interaction screens in yeast123,124 have demonstrated that thousands of combinations of individually viable mutations can jointly be lethal, and similar examples have been documented in Drosophila melanogaster and Caenorhabditis elegans125,126.”

    From Rare and common variants: twenty arguments (2012) · cites this paper as [124]

  • Genes belonging to similar biological processes tend to share common genetic interactions.

    “Genes belonging to similar biological processes tend to share common genetic interactions, and genes encoding proteins that function together within the same pathway or complex display similar genetic interaction profiles (fig. S4)(1).”
  • Genetic interaction networks highlight mechanistic connections between genes and their corresponding pathways.

    “Genetic interaction networks highlight mechanistic connections between genes and their corresponding pathways (1).”
  • Synthetic genetic array (SGA) analysis automates the combinatorial construction of defined mutants and enables quantitative analysis of genetic interactions.

    “Synthetic genetic array (SGA) analysis automates the combinatorial construction of defined mutants and enables the quantitative analysis of genetic interactions (1, 5).”
  • Negative and positive genetic interactions were quantified and false negative/positive rates and data reproducibility were determined at defined confidence thresholds from analysis of biological replicates and comparison of interactions for a subset of gene pairs represented on both mutant arrays.

    “Negative and positive genetic interactions were quantified and false negative/positive rates and data reproducibility were determined at defined confidence thresholds (1) from analysis of biological replicates and comparison of interactions for a subset of gene pairs represented on both mutant arrays (fig. S2)(8).”

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Authors
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L. Y., Toufighi, K., Mostafavi, S., Prinz, J., St. Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z.-Y., Liang, W., Marback, M., Paw, J., San Luis, B.-J., Shuteriqi, E., Tong, A. H. Y., van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A.-C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., & Boone, C.
Affiliations
  • University of Toronto (CA)
  • University of Minnesota (US)
  • Massachusetts Institute of Technology (US)
  • Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
  • Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  • Harvard University (US)
  • Mount Sinai Hospital (CA)
  • University of California, Santa Cruz (US)
  • S&P Robotics, Inc., 1181 Finch Avenue West, North York, Ontario M3J 2V8, Canada.
  • Institute of Biochemistry (HU)
  • Princeton University (US)
  • McGill University (CA)
Corresponding author
  • Costanzo, Michael
  • Baryshnikova, Anastasia
  • Myers, Chad L.
  • Andrews, Brenda J.
  • Boone, Charles
Venue
Science
Published
2010-01-22
Volume
327
Issue
5964
Pages
425-431
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W2133102806
Cited by
2,162
References
38
Citations by year
2026: 36 · 2025: 48 · 2024: 57 · 2023: 70 · 2022: 75 · 2021: 83 · 2020: 93 · 2019: 98 · 2018: 115 · 2017: 159 · 2016: 161 · 2015: 183 · 2014: 203 · 2013: 212 · 2012: 212
FWCI
101.56
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Wellcome Trust (084314)
  • Canadian Institutes of Health Research (GSP-415-67)
  • National Human Genome Research Institute (R01HG003224)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords
synthetic genetic interactions, gene-gene interaction, genetic interaction networks, Saccharomyces cerevisiae, gene function annotation, pleiotropy, chemical-genetic interactions, drug target identification
MeSH terms
Genes, Fungal, Mutation, Saccharomyces cerevisiae, Gene Expression Regulation, Fungal, Genome, Fungal, Computational Biology, Gene Duplication, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Gene Regulatory Networks, Metabolic Networks and Pathways, Genetic Fitness

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