Pattern Matching in Protein-Protein Interaction Graphs

Gaëlle Brevier-Giberti (1) , Roméo Rizzi (2) , Stéphane Vialette (3)

1 G-SCOP_GCSP - Gestion et Conduite des Systèmes de Production
2 DIMI - Dipartimento di Matematica e Informatica - Universita Udine
3 Algorithmics

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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Combinatoire [math.CO]; Algorithme et structure de données [cs.DS]; Complexité [cs.CC]; Mathématique discrète [cs.DM]

Gaëlle Brevier-Giberti, Roméo Rizzi, Stéphane Vialette. Pattern Matching in Protein-Protein Interaction Graphs. FCT 2007, Aug 2007, Budapest, Hungary. pp.137-148, ⟨10.1007/978-3-540-74240-1_13⟩. ⟨hal-00199009⟩