title: FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks.
abstract: The characterization of the interacting behaviors of complex biological systems is a primary objective in protein-protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in diseases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.
authors.affiliation: Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy. Electronic address: massimo.natale@polito.it.
authors.forename: Massimo
authors.initials: M
authors.lastname: Natale
authors.affiliation: Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Benso
authors.affiliation: Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Di Carlo
authors.affiliation: Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Ficarra
mesh_terms: D019295:Computational Biology; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins
keywords: Budd–Chiari syndrome; Cytoscape; Network analysis; Network modules; Pathway analysis; Systems biology