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  Cluster-based assessment of protein-protein interaction confidence

Kamburov, A., Grossmann, A., Herwig, R., & Stelzl, U. (2012). Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics, 13:262 -13:262. doi:10.1186/1471-2105-13-262.

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1471-2105-13-262.pdf (Verlagsversion), 1003KB
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© 2012 Kamburov et al.; licensee BioMed Central Ltd.
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Kamburov, Atanas1, Autor           
Grossmann, Arndt2, Autor           
Herwig, Ralf1, Autor           
Stelzl, Ulrich2, Autor           
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
2Molecular Interaction Networks (Ulrich Stelzl), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479660              

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 Zusammenfassung: Background: Protein-protein interaction networks are key to a systems-level understanding of cellular biology. However, interaction data can contain a considerable fraction of false positives. Several methods have been proposed to assess the confidence of individual interactions. Most of them require the integration of additional data like protein expression and interaction homology information. While being certainly useful, such additional data are not always available and may introduce additional bias and ambiguity. Results: We propose a novel, network topology based interaction confidence assessment method called CAPPIC (cluster-based assessment of protein-protein interaction confidence). It exploits the network’s inherent modular architecture for assessing the confidence of individual interactions. Our method determines algorithmic parameters intrinsically and does not require any parameter input or reference sets for confidence scoring. Conclusions: On the basis of five yeast and two human physical interactome maps inferred using different techniques, we show that CAPPIC reliably assesses interaction confidence and its performance compares well to other approaches that are also based on network topology. The confidence score correlates with the agreement in localization and biological process annotations of interacting proteins. Moreover, it corroborates experimental evidence of physical interactions. Our method is not limited to physical interactome maps as we exemplify with a large yeast genetic interaction network. An implementation of CAPPIC is available at http://intscore.molgen.mpg.de

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 Datum: 2012-10-12
 Publikationsstatus: Online veröffentlicht
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 Identifikatoren: DOI: 10.1186/1471-2105-13-262
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Titel: BMC Bioinformatics
Genre der Quelle: Zeitschrift
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Seiten: - Band / Heft: - Artikelnummer: - Start- / Endseite: 13:262 - 13:262 Identifikator: ISSN: 1471-2105
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905000