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A cytoscape based framework for efficient sub-graph isomorphic protein-protein interaction motif lookup

Study of interactomes requires assembling complex tools, ontologies and online interaction network databases and so on to validate hypotheses and gain insight. One of the major bottlenecks is the discovery of similar or isomorphic subgraphs in very large interactomes and cross referencing the relationships a set of proteins or genes share. These interactomes are so large that most traditional subgraph isomorphism computation tools are unable to handle efficiently as stand alone tool, or as part of systems such as R. In this paper, we present a Cytoscape plugin to compute and discover isomorphic subnetworks in large interactomes based on a novel and efficient isomorphic subgraph computation method developed in our laboratory. Given an input interactome and a given query subnetwork, the plugin can efficiently compute interactome subnetworks similar to the query network, and cross reference the results from GO or other interactome databases with the aid of other available Cytoscape plugins such as BinGO. We describe the tool with respect to real life applications Biologists may want to contemplate.