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An empirical framework for binary interactome mapping

Kavitha Venkatesan, Jean-Francois Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens UGent, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il Goh, et al. (2009) NATURE METHODS. 6(1). p.83-90
abstract
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
RESOURCE, PROTEOMICS, MOLECULAR INTERACTION DATABASE, PROTEIN-PROTEIN INTERACTIONS, YEAST, INTERACTION NETWORK, MAP
journal title
NATURE METHODS
Nat. Methods
volume
6
issue
1
pages
83 - 90
publisher
NATURE PUBLISHING GROUP
place of publication
LONDON N1 9XW, ENGLAND
Web of Science type
Article
Web of Science id
000262370200030
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
16.874 (2009)
JCR rank
1/65 (2009)
JCR quartile
1 (2009)
ISSN
1548-7091
DOI
10.1038/NMETH.1280
language
English
UGent publication?
yes
classification
A1
id
539289
handle
http://hdl.handle.net/1854/LU-539289
date created
2009-04-07 15:01:54
date last changed
2017-01-02 09:55:36
@article{539289,
  abstract     = {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.},
  author       = {Venkatesan, Kavitha and Rual, Jean-Francois and Vazquez, Alexei and Stelzl, Ulrich and Lemmens, Irma and Hirozane-Kishikawa, Tomoko and Hao, Tong and Zenkner, Martina and Xin, Xiaofeng and Goh, Kwang-Il and Yildirim, Muhammed A. and Simonis, Nicolas and Heinzmann, Kathrin and Gebreab, Fana and Sahalie, Julie M and Cevik, Sebiha and Simon, Christophe and De Smet, Anne-Sophie and Dann, Elizabeth and Smolyar, Alex and Vinayagam, Arunachalam and Yu, Haiyuan and Szeto, David and Borick, Heather and Dricot, Amelie and Klitgord, Niels and Murray, Ryan R. and Lin, Chenwei and Lalowski, Maciej and Timm, Jan and Rau, Kirstin and Boone, Charles and Braun, Pascal and Cusick, Michael E. and Roth, Frederick P. and Hill, David E. and Tavernier, Jan and Wanker, Erich E. and Barabasi, Albert-Laszlo and Vidal, Marc},
  issn         = {1548-7091},
  journal      = {NATURE METHODS},
  keyword      = {RESOURCE,PROTEOMICS,MOLECULAR INTERACTION DATABASE,PROTEIN-PROTEIN INTERACTIONS,YEAST,INTERACTION NETWORK,MAP},
  language     = {eng},
  number       = {1},
  pages        = {83--90},
  publisher    = {NATURE PUBLISHING GROUP},
  title        = {An empirical framework for binary interactome mapping},
  url          = {http://dx.doi.org/10.1038/NMETH.1280},
  volume       = {6},
  year         = {2009},
}

Chicago
Venkatesan, Kavitha, Jean-Francois Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, et al. 2009. “An Empirical Framework for Binary Interactome Mapping.” Nature Methods 6 (1): 83–90.
APA
Venkatesan, K., Rual, J.-F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., et al. (2009). An empirical framework for binary interactome mapping. NATURE METHODS, 6(1), 83–90.
Vancouver
1.
Venkatesan K, Rual J-F, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, et al. An empirical framework for binary interactome mapping. NATURE METHODS. LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP; 2009;6(1):83–90.
MLA
Venkatesan, Kavitha, Jean-Francois Rual, Alexei Vazquez, et al. “An Empirical Framework for Binary Interactome Mapping.” NATURE METHODS 6.1 (2009): 83–90. Print.