Identifying Sub-Network Functional Modules in Protein Undirected Networks

Protein networks are usually used to describe the interacting behaviours of complex biosystems. Bioinformatics must be able to provide methods to mine protein undirected networks and to infer subnetworks of interacting proteins for identifying relevant biological pathways. Here we present FunMod an innovative Cytoscape version 2.8 plugin able to identify biologically significant sub-networks within informative protein networks, enabling new opportunities for elucidating pathways involved in diseases. Moreover FunMod calculates three topological coefficients for each subnetwork, for a better understanding of the cooperative interactions between proteins and discriminating the role played by each protein within a functional module. FunMod is the first Cytoscape plugin with the ability of combining pathways and topological analysis allowing the identification of the key proteins within sub-network functional modules.