Modular decomposition of protein-protein interaction networks
1 Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
2 Laboratoire de Mathématiques Appliquées aux Systèmes, Ecole Centrale Paris, Grande Voie des Vignes, 92295 Châtenay-Malabry cedex, France
Genome Biology 2004, 5:R57 doi:10.1186/gb-2004-5-8-r57Published: 21 July 2004
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.