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

Nicolas Simonis, Jean-Francois Rual, Anne-Ruxandra Carvunis, Murat Tasan, Irma Lemmens UGent, Tomoko Hirozane-Kishikawa, Tong Hao, Julie M. Sahalie, Kavitha Venkatesan, Fana Gebreab, et al. (2009) NATURE METHODS. 6(1). p.47-54
abstract
Abstract: 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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PERTURBATION, INTERACTION MAP, RESOURCE, SEQUENCE, EARLY EMBRYOGENESIS, C-ELEGANS, ANNOTATION
journal title
NATURE METHODS
Nat. Methods
volume
6
issue
1
pages
47 - 54
publisher
NATURE PUBLISHING GROUP
place of publication
4 CRINAN ST, LONDON N1 9XW, ENGLAND
Web of Science type
Article
Web of Science id
000262370200023
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.1279
language
English
UGent publication?
yes
classification
A1
id
603071
handle
http://hdl.handle.net/1854/LU-603071
date created
2009-04-28 16:24:59
date last changed
2017-01-02 09:57:04
@article{603071,
  abstract     = {Abstract: 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.},
  author       = {Simonis, Nicolas and Rual, Jean-Francois and Carvunis, Anne-Ruxandra and Tasan, Murat and Lemmens, Irma and Hirozane-Kishikawa, Tomoko and Hao, Tong and Sahalie, Julie M. and Venkatesan, Kavitha and Gebreab, Fana and Cevik, Sebiha and Klitgord, Niels and Fan, Changyu and Braun, Pascal and Li, Ning and Ayivi-Guedehoussou, Nono and Dann, Elizabeth and Bertin, Nicolas and Szeto, David and Dricot, Ameli and Yildirim, Muhammed A. and Lin, Chenwei and De Smet, Anne-Sophie and Kao, Huey-Ling and Simon, Christophe and Smolyar, Alex and Ahn, Jin Sook and Tewari, Muneesh and Boxem, Mike and Milstein, Stuart and Yu, Haiyuan and Dreze, Matija and Vandenhaute, Jean and Gunsalus, Kristin C. and Cusick, Michael E. and Hill, David E. and Tavernier, Jan and Roth, Frederick P. and Vidal, Marc},
  issn         = {1548-7091},
  journal      = {NATURE METHODS},
  keyword      = {PERTURBATION,INTERACTION MAP,RESOURCE,SEQUENCE,EARLY EMBRYOGENESIS,C-ELEGANS,ANNOTATION},
  language     = {eng},
  number       = {1},
  pages        = {47--54},
  publisher    = {NATURE PUBLISHING GROUP},
  title        = {Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network},
  url          = {http://dx.doi.org/10.1038/NMETH.1279},
  volume       = {6},
  year         = {2009},
}

Chicago
Simonis, Nicolas, Jean-Francois Rual, Anne-Ruxandra Carvunis, Murat Tasan, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, et al. 2009. “Empirically Controlled Mapping of the Caenorhabditis Elegans Protein-protein Interactome Network.” Nature Methods 6 (1): 47–54.
APA
Simonis, N., Rual, J.-F., Carvunis, A.-R., Tasan, M., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., et al. (2009). Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. NATURE METHODS, 6(1), 47–54.
Vancouver
1.
Simonis N, Rual J-F, Carvunis A-R, Tasan M, Lemmens I, Hirozane-Kishikawa T, et al. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. NATURE METHODS. 4 CRINAN ST, LONDON N1 9XW, ENGLAND: NATURE PUBLISHING GROUP; 2009;6(1):47–54.
MLA
Simonis, Nicolas, Jean-Francois Rual, Anne-Ruxandra Carvunis, et al. “Empirically Controlled Mapping of the Caenorhabditis Elegans Protein-protein Interactome Network.” NATURE METHODS 6.1 (2009): 47–54. Print.