Protein-protein interaction network querying by a "focus and zoom" approach

Abstract

We propose an approach to network querying in proteinprotein interaction networks based on bipartite graph weighted matching. An algorithm is presented that first "focuses" the potentially relevant portion of the target graph by performing a global alignment of this one with the query graph, and then "zooms" on the actual matching nodes by considering their topological arrangement, hereby obtaining a (possibly) approximated occurrence of the query graph within the target graph. Approximation is related to node insertions, node deletions and edge deletions possibly intervening in the query graph. The technique manages networks of arbitrary topology. Moreover, edge labels are used to represent and manage the reliability of involved interactions. Some preliminary experimental analysis is also accounted for in the paper. © Springer-Verlag Berlin Heidelberg 2008.