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          Institute: MPI für Infektionsbiologie     Collection: Department of Cellular Microbiology     Display Documents

ID: 335196.0, MPI für Infektionsbiologie / Department of Cellular Microbiology
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
Authors:Rungsarityotin, Wasinee; Krause, Roland; Schödl, Arno; Schliep, Alexander
Date of Publication (YYYY-MM-DD):2007-12-19
Title of Journal:BMC Bioinformatics
Issue / Number:Article Number: 482
Start Page:1
End Page:19
Copyright:© 2007 Rungsarityotin et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Review Status:not specified
Audience:Experts Only
Abstract / Description:Background
Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rely on a two-step process. First, they construct an interaction graph from the data, predominantly using heuristics, and subsequently cluster its vertices to identify protein complexes.

We propose a model-based identification of protein complexes directly from the experimental observations. Our model of protein complexes based on Markov random fields explicitly incorporates false negative and false positive errors and exhibits a high robustness to noise. A model-based quality score for the resulting clusters allows us to identify reliable predictions in the complete data set. Comparisons with prior work on reference data sets shows favorable results, particularly for larger unfiltered data sets. Additional information on predictions, including the source code under the GNU Public License can be found at http://algorithmics.molgen.mpg.de/Static/Supplements/ProteinComplexes.

We can identify complexes in the data obtained from high-throughput experiments without prior elimination of proteins or weak interactions. The few parameters of our model, which does not rely on heuristics, can be estimated using maximum likelihood without a reference data set. This is particularly important for protein complex studies in organisms that do not have an established reference frame of known protein complexes.
Comment of the Author/Creator:Acknowledgements
This work was supported by the Institute for Pure and Applied Mathematics (IPAM) of the UCLA.
External Publication Status:published
Document Type:Article
Communicated by:Hilmar Fünning
Affiliations:MPI für Infektionsbiologie/Department of Cellular Microbiology
MPI für molekulare Genetik
External Affiliations:Think-cell software, Invalidenstr. 43, D-10115 Berlin, Germany
Identifiers:ISSN:1471-2105 [ID No:1]
DOI:10.1186/1471-2105-8-482 [ID No:2]
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