Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs

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-($\mu$G; $\mu$H)-Matching problem and the Max-($\mu$G; $\mu$H)-Matching problems, where $\mu$G (resp. $\mu$H) denotes in both problems the maximum number of orthologous proteins in H (resp. G) of a protein in G (resp. H). Following [10], the Exact-($\mu$G; $\mu$H)-Matching problem asks for an injective homomorphism of G to H w.r.t. orthologous proteins. The optimization version is called the Max-($\mu$G; $\mu$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 $\mu$G and $\mu$H.
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Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs. Journal of Discrete Algorithms, Elsevier, 2009, 7 (1), pp.90-101. ⟨hal-00416394⟩

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