Cited by 1,392Bioinformatics and Genomic NetworksFungal and yeast genetics researchAdvanced Proteomics Techniques and Applications

The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

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Abstract

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a “second-generation” high-quality, high-throughput Y2H data set covering ∼20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.

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  1. I. Remy, S. W. Michnick, Methods Mol. Biol.261, 411 (2004).
  2. A. M. Dudley, D. M. Janse, A. Tanay, R. Shamir, G. M. Church, Mol. Syst. Biol.1, 0001 (2005).

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Metadata

Authors
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J.-F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A.-S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabási, A.-L., Tavernier, J., Hill, D. E., & Vidal, M.
Affiliations
  • Harvard University (US)
  • Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02115, USA.
  • Northeastern University (US)
Corresponding author
  • Yu, Haiyuan
  • Yıldırım, Muhammed A.
  • Vidal, Marc
Venue
Science
Published
2008-10-03
Volume
322
Issue
5898
Pages
104-110
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W2109248504
Cited by
1,392
References
45
Citations by year
2026: 18 · 2025: 26 · 2024: 29 · 2023: 34 · 2022: 63 · 2021: 55 · 2020: 66 · 2019: 65 · 2018: 67 · 2017: 72 · 2016: 68 · 2015: 78 · 2014: 79 · 2013: 122 · 2012: 172
FWCI
51.78
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion)
  • Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
Funders
  • U.S. Public Health Service (U01A1070499-01)
  • National Human Genome Research Institute (R01HG001715, R01HG003224, HG003224)
  • National Cancer Institute (U56CA113004)
  • National Institute of Allergy and Infectious Diseases (U01AI070499)
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
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Keywords
yeast interactome, protein-protein interaction network, yeast two-hybrid screening, affinity purification mass spectrometry, protein complexes, essential proteins, protein connectivity, pleiotropy, network topology
MeSH terms
Protein Binding, Saccharomyces cerevisiae, Mass Spectrometry, Transcription Factors, Signal Transduction, Computational Biology, Proteome, Two-Hybrid System Techniques, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Protein Array Analysis, Proteomics, Gene Regulatory Networks, Metabolic Networks and Pathways

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