Mirco Gerke^1,2, Erich Bornberg-Bauer¹, Xiaoyi Jiang² and Georg Fuellen^1,3

¹Division of Bioinformatics, Biology Department, Schlossplatz 4, D-48149 Münster, Germany; ²Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, D- 48149 Münster, Germany; ³Department of Medicine, AG Bioinformatics, Domagkstr. 3, D-48149 Münster, Germany

Abstract: Protein interactions are an important resource to obtain an understanding of cell function. Recently, researchers have compared networks of interactions in order to understand network evolution. While current methods first infer homologs and then compare topologies, we here present a method which first searches for interesting topologies and then looks for homologs. PINA (protein interaction network analysis) takes the protein interaction networks of two organisms, scans both networks for subnetworks deemed interesting, and then tries to find orthologs among the interesting subnetworks. The application is very fast because orthology investigations are restricted to subnetworks like hubs and clusters that fulfill certain criteria regarding neighborhood and connectivity. Finally, the hubs or clusters found to be related can be visualized and analyzed according to protein annotation.