Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

被引：216

作者：

Simonis, Nicolas ^{[1
,2
,3
]}

Rual, Jean-Francois ^{[1
,2
,3
]}

Carvunis, Anne-Ruxandra ^{[1
,2
,3
,4
]}

Tasan, Murat ^{[5
]}

Lemmens, Irma ^{[6
,7
]}

Hirozane-Kishikawa, Tomoko ^{[1
,2
,3
]}

Hao, Tong ^{[1
,2
,3
]}

Sahalie, Julie M. ^{[1
,2
,3
]}

Venkatesan, Kavitha ^{[1
,2
,3
]}

Gebreab, Fana ^{[1
,2
,3
]}

Cevik, Sebiha ^{[1
,2
,3
]}

Klitgord, Niels ^{[1
,2
,3
]}

Fan, Changyu ^{[1
,2
,3
]}

Braun, Pascal ^{[1
,2
,3
]}

Li, Ning ^{[1
,2
,3
]}

Ayivi-Guedehoussou, Nono ^{[1
,2
,3
]}

Dann, Elizabeth ^{[1
,2
,3
]}

Bertin, Nicolas ^{[1
,2
,3
]}

Szeto, David ^{[1
,2
,3
]}

Dricot, Ameli ^{[1
,2
,3
]}

Yildirim, Muhammed A. ^{[1
,2
,3
,8
]}

Lin, Chenwei ^{[1
,2
,3
]}

de Smet, Anne-Sophie

Kao, Huey-Ling ^{[9
]}

Simon, Christophe ^{[1
,2
,3
]}

Smolyar, Alex ^{[1
,2
,3
]}

Ahn, Jin Sook ^{[1
,2
,3
]}

Tewari, Muneesh ^{[1
,2
,3
]}

Boxem, Mike ^{[1
,2
,3
,10
]}

Milstein, Stuart ^{[1
,2
,3
]}

Yu, Haiyuan ^{[1
,2
,3
]}

Dreze, Matija ^{[1
,2
,3
,11
]}

Vandenhaute, Jean ^{[11
]}

Gunsalus, Kristin C. ^{[9
]}

Cusick, Michael E. ^{[1
,2
,3
]}

Hill, David E. ^{[1
,2
,3
]}

Tavernier, Jan ^{[6
,7
]}

Roth, Frederick P. ^{[1
,2
,5
]}

Vidal, Marc ^{[1
,2
,3
]}

机构：

[1] Dana Farber Canc Inst, CCSB, Boston, MA 02115 USA

[2] Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02115 USA

[3] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[4] Univ Grenoble 1, Fac Med, CNRS, TIMC IMAG,Unite Mixte Rech 5525, F-38706 La Tronche, France

[5] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA

[6] Univ Ghent, Fac Med & Hlth Sci, Vlaams Inst Biotechnol, Dept Med Prot Res, B-9000 Ghent, Belgium

[7] Univ Ghent, Fac Med & Hlth Sci, Dept Biochem, B-9000 Ghent, Belgium

[8] Harvard Univ, Div Engn & Appl Sci, Cambridge, MA 02138 USA

[9] NYU, Dept Biol, Ctr Genom & Syst Biol, New York, NY 10003 USA

[10] Massachusetts Gen Hosp, Ctr Canc Res, Boston, MA 02129 USA

[11] Fac Univ Notre Dame Paix, Unite Rech Biol Mol, B-5000 Namur, Belgium

来源：

NATURE METHODS | 2009年 / 6卷 / 01期

基金：

美国国家卫生研究院;

关键词：

C-ELEGANS; INTERACTION MAP; PERTURBATION; ANNOTATION; RESOURCE; SEQUENCE;

D O I：

10.1038/NMETH.1279

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards. We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of similar to 10,000 x similar to 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set ( Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map ( Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at similar to 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins.

引用

页码：47 / 54

页数：8

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