The characterization of the interacting behaviors of complex biological systems is a primary objective in protein–protein network analysis and computational biology. FunMod, is 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.
Developers
How to cite FunMOD
The SysBio development team has invested a lot of time and effort in creating FunMOD as it is today. Please give credit where credit is due and cite FunMOD when you use it for your research activities.
FunMOD can be cited through this papers:
Massimo Natale, Alfredo Benso, Stefano Di Carlo, Elisa Ficarra, FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks, Genomics, Proteomics & Bioinformatics, Volume 12, Issue 4, August 2014, Pages 178-186, ISSN 1672-0229, http://dx.doi.org/10.1016/j.gpb.2014.05.002.
(http://www.sciencedirect.com/science/article/pii/S1672022914000795)
BibTEX
@article{Natale2014178,
title = "FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks ",
journal = "Genomics, Proteomics & Bioinformatics ",
volume = "12",
number = "4",
pages = "178 - 186",
year = "2014",
note = "",
issn = "1672-0229",
doi = "http://dx.doi.org/10.1016/j.gpb.2014.05.002",
url = "http://www.sciencedirect.com/science/article/pii/S1672022914000795",
author = "Massimo Natale and Alfredo Benso and Stefano Di Carlo and Elisa Ficarra",
}