Finding occurrences of protein complexes in protein-protein interaction graphs

  • Authors:

  • Guillaume Fertin;Romeo Rizzi;Stéphane Vialette

  • Affiliations:

  • Laboratoire d'Informatique de Nantes-Atlantique (LINA), CNRS UMR 6241, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France;Dipartimento di Matematica ed Informatica (DIMI), Universití di Udine, Via delle Scienze 208, I-33100 Udine, Italy;IGM-LabInfo, CNRS UMR 8049, Université Paris-Est, 5 Bd Descartes 77454 Marne-la-Vallée, France

  • Venue:
  • Journal of Discrete Algorithms
  • Year:
  • 2009

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Abstract

In the context of comparative analysis of protein-protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex G in the protein-protein interaction graph H of another species with respect to (w.r.t.) orthologous proteins. Two problems are considered: the Exact-(@m"G,@m"H)-Matching problem and the Max-(@m"G,@m"H)-Matching problems, where @m"G (resp. @m"H) denotes in both problems the maximum number of orthologous proteins in H (resp. G) of a protein in G (resp. H). Following [I. Fagnot, G. Lelandais, S. Vialette, Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs, Journal of Discrete Algorithms 6 (2) (2008) 178-191], the Exact-(@m"G,@m"H)-Matching problem asks for an injective homomorphism of G to H w.r.t. orthologous proteins. The optimization version is called the Max-(@m"G,@m"H)-Matching problem and is concerned with finding an injective mapping of a graph G to a graph H w.r.t. orthologous proteins that matches as many edges of G as possible. For both problems, we essentially focus on bounded degree graphs and extremal small values of parameters @m"G and @m"H.