  MethodModular decomposition of protein-protein interaction networksJulien Gagneur1,2  , Roland Krause1, Tewis Bouwmeester1 and Georg Casari1 1Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany 2Laboratoire de Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Grande Voie des Vignes, 92295 Châtenay-Malabry cedex, France  author email corresponding author email
Genome Biology 2004,
5:R57doi:10.1186/gb-2004-5-8-r57
Subject areas: Bioinformatics, Methods, Biochemistry and structural biology Abstract
We introduce an algorithmic method, termed modular decomposition, that defines the organization of protein-interaction networks as a hierarchy of nested modules. Modular decomposition derives the logical rules of how to combine proteins into the actual functional complexes by identifying groups of proteins acting as a single unit (sub-complexes) and those that can be alternatively exchanged in a set of similar complexes. The method is applied to experimental data on the pro-inflammatory tumor necrosis factor-α (TNF-α)/NFκB transcription factor pathway. | 
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