A rule-based detection of functional modules in protein-protein interaction networks.

In the protein-protein interaction (PPI) network there are many functional modules, each involving several protein interactions to perform discrete functions. Pathways and protein complexes are the examples of the functional modules. In this paper, we propose a rule-based method for detecting the modules. The rule is expressed in terms of triples and operators between the triples. The former represents conceptual relations reifying the protein interactions of a module, and the latter defines the structure of the module with the relations. Additionally, users can define composite rules by composing the predefined rules. The composite rules make it possible to detect modules that are conceptually similar as well as structurally identical to users' queries. The rules are managed in the XML format so that they can be easily applied to other networks of different species. We also provide a visualized environment for intuitionally describing complexly structured rules.