An empirical framework for binary interactome mapping

Kavitha Venkatesan, Jean François Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il Goh, Muhammed A. Yildirim, Nicolas Simonis, Kathrin Heinzmann, Fana Gebreab, Julie M. Sahalie, Sebiha Cevik, Christophe Simon, Anne Sophie de Smet, Elizabeth Dann, Alex SmolyarArunachalam Vinayagam, Haiyuan Yu, David Szeto, Heather Borick, Amélie Dricot, Niels Klitgord, Ryan R. Murray, Chenwei Lin, Maciej Lalowski, Jan Timm, Kirstin Rau, Charles Boone, Pascal Braun, Michael E. Cusick, Frederick P. Roth, David E. Hill, Jan Tavernier, Erich E. Wanker, Albert László Barabási, Marc Vidal

Research output: Contribution to journalArticle

528 Citations (Scopus)

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 ∼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.

Original languageEnglish
Pages (from-to)83-90
Number of pages8
JournalNature Methods
Volume6
Issue number1
DOIs
Publication statusPublished - 2009 Jan 1

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Proteins
Genes
DNA sequences
Human Genome Project
Protein Interaction Maps
Genome Size
Yeast
Throughput
Publications
Yeasts
Data Accuracy
Datasets

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Venkatesan, K., Rual, J. F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane-Kishikawa, T., ... Vidal, M. (2009). An empirical framework for binary interactome mapping. Nature Methods, 6(1), 83-90. https://doi.org/10.1038/nmeth.1280

An empirical framework for binary interactome mapping. / Venkatesan, Kavitha; Rual, Jean François; Vazquez, Alexei; Stelzl, Ulrich; Lemmens, Irma; Hirozane-Kishikawa, Tomoko; Hao, Tong; Zenkner, Martina; Xin, Xiaofeng; Goh, Kwang-Il; Yildirim, Muhammed A.; Simonis, Nicolas; Heinzmann, Kathrin; Gebreab, Fana; Sahalie, Julie M.; Cevik, Sebiha; Simon, Christophe; de Smet, Anne Sophie; Dann, Elizabeth; Smolyar, Alex; Vinayagam, Arunachalam; Yu, Haiyuan; Szeto, David; Borick, Heather; Dricot, Amélie; Klitgord, Niels; Murray, Ryan R.; Lin, Chenwei; Lalowski, Maciej; Timm, Jan; Rau, Kirstin; Boone, Charles; Braun, Pascal; Cusick, Michael E.; Roth, Frederick P.; Hill, David E.; Tavernier, Jan; Wanker, Erich E.; Barabási, Albert László; Vidal, Marc.

In: Nature Methods, Vol. 6, No. 1, 01.01.2009, p. 83-90.

Research output: Contribution to journalArticle

Venkatesan, K, Rual, JF, Vazquez, A, Stelzl, U, Lemmens, I, Hirozane-Kishikawa, T, Hao, T, Zenkner, M, Xin, X, Goh, K-I, Yildirim, MA, Simonis, N, Heinzmann, K, Gebreab, F, Sahalie, JM, Cevik, S, Simon, C, de Smet, AS, Dann, E, Smolyar, A, Vinayagam, A, Yu, H, Szeto, D, Borick, H, Dricot, A, Klitgord, N, Murray, RR, Lin, C, Lalowski, M, Timm, J, Rau, K, Boone, C, Braun, P, Cusick, ME, Roth, FP, Hill, DE, Tavernier, J, Wanker, EE, Barabási, AL & Vidal, M 2009, 'An empirical framework for binary interactome mapping', Nature Methods, vol. 6, no. 1, pp. 83-90. https://doi.org/10.1038/nmeth.1280
Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T et al. An empirical framework for binary interactome mapping. Nature Methods. 2009 Jan 1;6(1):83-90. https://doi.org/10.1038/nmeth.1280
Venkatesan, Kavitha ; Rual, Jean François ; Vazquez, Alexei ; Stelzl, Ulrich ; Lemmens, Irma ; Hirozane-Kishikawa, Tomoko ; Hao, Tong ; Zenkner, Martina ; Xin, Xiaofeng ; Goh, Kwang-Il ; Yildirim, Muhammed A. ; Simonis, Nicolas ; Heinzmann, Kathrin ; Gebreab, Fana ; Sahalie, Julie M. ; Cevik, Sebiha ; Simon, Christophe ; de Smet, Anne Sophie ; Dann, Elizabeth ; Smolyar, Alex ; Vinayagam, Arunachalam ; Yu, Haiyuan ; Szeto, David ; Borick, Heather ; Dricot, Amélie ; Klitgord, Niels ; Murray, Ryan R. ; Lin, Chenwei ; Lalowski, Maciej ; Timm, Jan ; Rau, Kirstin ; Boone, Charles ; Braun, Pascal ; Cusick, Michael E. ; Roth, Frederick P. ; Hill, David E. ; Tavernier, Jan ; Wanker, Erich E. ; Barabási, Albert László ; Vidal, Marc. / An empirical framework for binary interactome mapping. In: Nature Methods. 2009 ; Vol. 6, No. 1. pp. 83-90.
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