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PMID: 18719252 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

High-quality binary protein interaction map of the yeast interactome network.

Science (New York, N.Y.) ·Vol. 322 ·No. 5898 ·2008-10-03 ·Pages 104-10

Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M

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 approximately 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.

MeSH Terms
Computational Biology Gene Regulatory Networks Mass Spectrometry Metabolic Networks and Pathways Protein Array Analysis Protein Binding Protein Interaction Mapping/methods,standards Proteome/metabolism Proteomics Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,isolation & purification,metabolism Signal Transduction Transcription Factors/metabolism Two-Hybrid System Techniques
Chemicals
Proteome Saccharomyces cerevisiae Proteins Transcription Factors
Authors & Affiliations
34 authors, click to expand affiliations / ORCID
Yu Haiyuan
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Braun Pascal
Yildirim Muhammed A
Lemmens Irma
Venkatesan Kavitha
Sahalie Julie
Hirozane-Kishikawa Tomoko
Gebreab Fana
Li Na
Simonis Nicolas
Hao Tong
Rual Jean-François
Dricot Amélie
Vazquez Alexei
Murray Ryan R
Simon Christophe
Tardivo Leah
Tam Stanley
Svrzikapa Nenad
Fan Changyu
de Smet Anne-Sophie
Motyl Adriana
Hudson Michael E
Park Juyong
Xin Xiaofeng
Cusick Michael E
Moore Troy
Boone Charlie
Snyder Michael
Roth Frederick P
Barabási Albert-László
Tavernier Jan
Hill David E
Vidal Marc
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Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1158684
Published
2008-10-03
Epub
2008-00-21
Pages
104-10
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC2746753
Subset
IM
Grants
NCI NIH HHS · U56 CA113004 · United States
NHGRI NIH HHS · R01 HG001715 · United States
NHGRI NIH HHS · R01 HG001715-06 · United States
NHGRI NIH HHS · R01 HG003224-04 · United States
PHS HHS · U01-A1070499-01 · United States
NHGRI NIH HHS · HG003224 · United States
NHGRI NIH HHS · R01-HG001715 · United States
NCI NIH HHS · U56-CA113004 · United States
NHGRI NIH HHS · R01 HG003224 · United States
NIAID NIH HHS · U01 AI070499-01 · United States
NCI NIH HHS · U56 CA113004-03 · United States
Corrections
CommentIn
PMID: 18832636
External Links
PubMed source DOI: 10.1126/science.1158684 PMC Full Text View journal details
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