An empirical framework for binary interactome mapping

被引：489

作者：

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

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

Vazquez, Alexei ^{[1
,2
,4
,5
,6
]}

Stelzl, Ulrich ^{[7
,8
]}

Lemmens, Irma ^{[9
,10
]}

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

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

Zenkner, Martina ^{[7
]}

Xin, Xiaofeng ^{[11
,12
]}

Goh, Kwang-Il ^{[1
,2
,4
,5
,13
]}

Yildirim, Muhammed A. ^{[1
,2
,3
,14
]}

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

Heinzmann, Kathrin ^{[1
,2
,3
]}

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

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

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

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

de Smet, Anne-Sophie ^{[9
,10
]}

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

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

Vinayagam, Arunachalam ^{[7
]}

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

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

Borick, Heather ^{[1
,2
,3
]}

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

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

Murray, Ryan R. ^{[1
,2
,3
]}

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

Lalowski, Maciej ^{[7
]}

Timm, Jan ^{[7
]}

Rau, Kirstin ^{[7
]}

Boone, Charles ^{[11
,12
]}

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

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

Roth, Frederick P. ^{[1
,2
,15
]}

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

Tavernier, Jan ^{[9
,10
]}

Wanker, Erich E. ^{[7
]}

Barabasi, Albert-Laszlo ^{[1
,2
,4
,5
]}

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

机构：

[1] Dana Farber Canc Inst, Ctr Canc Syst Biol, 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 Notre Dame, Ctr Complex Network Res, Notre Dame, IN 46556 USA

[5] Univ Notre Dame, Dept Phys, Notre Dame, IN 46556 USA

[6] Inst Adv Study, Simons Ctr Syst Biol, Princeton, NJ 08540 USA

[7] Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany

[8] Max Planck Inst Mol Genet, Otto Warburg Lab, D-14195 Berlin, Germany

[9] Univ Ghent, Vlaams Inst Biotechnol, Dept Med Prot Res, B-9000 Ghent, Belgium

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

[11] Univ Toronto, Terrence Donnelly Ctr Cellular & Biomol Res, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada

[12] Univ Toronto, Terrence Donnelly Ctr Cellular & Biomol Res, Dept Mol Genet, Toronto, ON M5S 3E1, Canada

[13] Korea Univ, Dept Phys, Seoul 136713, South Korea

[14] Harvard Univ, Sch Engn & Appl Sci, Cambridge, MA 02138 USA

[15] Harvard Univ, Sch Med, Dept Biochem & Mol Pharmacol, Boston, MA 02115 USA

来源：

NATURE METHODS | 2009年 / 6卷 / 01期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

PROTEIN-PROTEIN INTERACTIONS; MOLECULAR INTERACTION DATABASE; INTERACTION NETWORK; YEAST; PROTEOMICS; RESOURCE; MAP;

D O I：

10.1038/NMETH.1280

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains similar to 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.

引用

页码：83 / 90

页数：8

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