Finding exact and maximum occurrences of protein complexes in protein-protein interaction graphs

  • Authors:

  • Guillaume Fertin;Romeo Rizzi;Stéphane Vialette

  • Affiliations:

  • Laboratoire d'Informatique de Nantes-Atlantique (LINA), FRE CNRS 2729, Université de Nantes, Nantes Cedex 3, France;Facoltà di Scienze – Dipartimento di Informatica e Telecomunicazioni, Università degli Studi di Trento, Povo – Trento, (TN), Italy;Laboratoire de Recherche en Informatique (LRI), UMR CNRS 8623, Faculté des Sciences d'Orsay, Université Paris-Sud, Orsay, France

  • Venue:
  • MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
  • Year:
  • 2005

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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-(μG, μH)-Matching problem and the Max-(μG, μH) problem, where μG (resp. μH) denotes in both problems the maximum number of orthologous proteins in H (resp. G) of a protein in G (resp. H). Following [FLV04], the Exact-(μG, μH)-Matching problem asks for an injective homomorphism of G to H w.r.t. orthologous proteins. The optimization version is called the Max-(μG, μH)-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, the emphasis here is clearly on bounded degree graphs and extremal small values of parameters μG and μH.