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Network Querying Techniques for PPI Network Comparison

The aim of this chapter is that of analyzing and comparing network querying techniques as applied to protein interaction networks. In the last few years, several automatic tools supporting knowledge discovery from available biological interaction data have been developed. In particular, network querying tools search a whole biological network to identify conserved occurrences of a query network module. The goal of such techniques is that of transferring biological knowledge. Indeed, the query subnetwork generally encodes a well-characterized functional module, and its occurrences in the queried network probably denote that this function is featured by the associated organism. The proposed analysis is intended to be useful to understand problems and research issues, state of the art and opportunities for researchers working in this research area.