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

Nicolas Simonis, Jean François Rual, Anne Ruxandra Carvunis, Murat Tasan, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Julie M. Sahalie, Kavitha Venkatesan, Fana Gebreab, Sebiha Cevik, Niels Klitgord, Changyu Fan, Pascal Braun, Ning Li, Nono Ayivi-Guedehoussou, Elizabeth Dann, Nicolas Bertin, David Szeto, Amélie DricotMuhammed A. Yildirim, Chenwei Lin, Anne Sophie de Smet, Huey Ling Kao, Christophe Simon, Alex Smolyar, Jin Sook Ahn, Muneesh Tewari, Mike Boxem, Stuart Milstein, Haiyuan Yu, Matija Dreze, Jean Vandenhaute, Kristin C. Gunsalus, Michael E. Cusick, David E. Hill, Jan Tavernier, Frederick P. Roth, Marc Vidal

Research output: Contribution to journalArticle

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 ∼10,000 × ∼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 ∼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.

Original languageEnglish (US)
Pages (from-to)47-54
Number of pages8
JournalNature methods
Volume6
Issue number1
DOIs
StatePublished - Jan 1 2009

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ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Simonis, N., Rual, J. F., Carvunis, A. R., Tasan, M., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., Sahalie, J. M., Venkatesan, K., Gebreab, F., Cevik, S., Klitgord, N., Fan, C., Braun, P., Li, N., Ayivi-Guedehoussou, N., Dann, E., Bertin, N., Szeto, D., ... Vidal, M. (2009). Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature methods, 6(1), 47-54. https://doi.org/10.1038/nmeth.1279