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Proc Natl Acad Sci U S A

Title:		Finding undetected protein associations in cell signaling by belief propagation
Author(s):		Bailly-Bechet M; Borgs C; Braunstein A; Chayes J; Dagkessamanskaia A; Francois JM; Zecchina R;
Address:		"Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, Villeurbanne, France"
Journal Title:		Proc Natl Acad Sci U S A
Year:		2011
Volume:		20101227
Issue:		2
Page Number:		882 - 887
DOI:		10.1073/pnas.1004751108
ISSN/ISBN:		1091-6490 (Electronic) 0027-8424 (Print) 0027-8424 (Linking)
Abstract:		"External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High-throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field"
Keywords:		"Adenosine Triphosphatases/chemistry Algorithms Alleles Biophysics/methods Computational Biology/*methods Endosomal Sorting Complexes Required for Transport/chemistry Models, Biological Models, Statistical Pheromones Plasmids/metabolism Protein Interaction;"
Notes:		"MedlineBailly-Bechet, M Borgs, C Braunstein, A Chayes, J Dagkessamanskaia, A Francois, J-M Zecchina, R eng Research Support, Non-U.S. Gov't 2010/12/29 Proc Natl Acad Sci U S A. 2011 Jan 11; 108(2):882-7. doi: 10.1073/pnas.1004751108. Epub 2010 Dec 27"