Modular decomposition of protein-protein interaction networks.
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-alpha (TNF-alpha)/NFkappaB transcription factor pathway.
Gagneur
Julien
J
Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany. julien.gagneur@cellzome.com
Krause
Roland
R
Bouwmeester
Tewis
T
Casari
Georg
G
D000465:Algorithms; D019295:Computational Biology; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects; D046912:Multiprotein Complexes / Q000737:chemistry / Q000378:metabolism; D016328:NF-kappa B / Q000378:metabolism; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000187:drug effects; D014157:Transcription Factors / Q000378:metabolism; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
D046912:Multiprotein Complexes; D016328:NF-kappa B; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D014409:Tumor Necrosis Factor-alpha; D012321:DNA-Directed RNA Polymerases