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FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks
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 a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411368/ https://www.ncbi.nlm.nih.gov/pubmed/25153667 http://dx.doi.org/10.1016/j.gpb.2014.05.002 |
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author | Natale, Massimo Benso, Alfredo Di Carlo, Stefano Ficarra, Elisa |
author_facet | Natale, Massimo Benso, Alfredo Di Carlo, Stefano Ficarra, Elisa |
author_sort | Natale, Massimo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4411368 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-44113682015-05-06 FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks Natale, Massimo Benso, Alfredo Di Carlo, Stefano Ficarra, Elisa Genomics Proteomics Bioinformatics Method 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. Elsevier 2014-08 2014-08-19 /pmc/articles/PMC4411368/ /pubmed/25153667 http://dx.doi.org/10.1016/j.gpb.2014.05.002 Text en © 2014 The Authors http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/). |
spellingShingle | Method Natale, Massimo Benso, Alfredo Di Carlo, Stefano Ficarra, Elisa FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title | FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title_full | FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title_fullStr | FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title_full_unstemmed | FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title_short | FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks |
title_sort | funmod: a cytoscape plugin for identifying functional modules in undirected protein–protein networks |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411368/ https://www.ncbi.nlm.nih.gov/pubmed/25153667 http://dx.doi.org/10.1016/j.gpb.2014.05.002 |
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