Pattern matching in protein-protein interaction graphs

Authors:
Gaëlle Brevier;Romeo Rizzi;Stéphane Vialette
Affiliations:
G-SCOP, Grenoble, France;Dipartimento di Matematica ed Informatica, Universit` di Udine, Italy;Laboratoire de Recherche en Informatique, UMR CNRS 8623, Université Paris-Sud 11, France
Venue:
FCT'07 Proceedings of the 16th international conference on Fundamentals of Computation Theory
Year:
2007

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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 (pattern graph) in the protein-protein interaction graph (target graph) of another species with respect to (w.r.t.) orthologous proteins. We give an efficient exponential-time randomized algorithm in case the occurrence of the pattern graph in the target graph is required to be exact. For approximate occurrences, we prove a tight inapproximability results and give four approximation algorithms that deal with bounded degree graphs, small ortholog numbers, linear forests and very simple yet hard instances, respectively.