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CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological n...

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Detalles Bibliográficos
Autores principales: Li, Min, Li, Dongyan, Tang, Yu, Wu, Fangxiang, Wang, Jianxin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5618529/
https://www.ncbi.nlm.nih.gov/pubmed/28858211
http://dx.doi.org/10.3390/ijms18091880
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author Li, Min
Li, Dongyan
Tang, Yu
Wu, Fangxiang
Wang, Jianxin
author_facet Li, Min
Li, Dongyan
Tang, Yu
Wu, Fangxiang
Wang, Jianxin
author_sort Li, Min
collection PubMed
description Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.
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spelling pubmed-56185292017-09-30 CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks Li, Min Li, Dongyan Tang, Yu Wu, Fangxiang Wang, Jianxin Int J Mol Sci Article Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster. MDPI 2017-08-31 /pmc/articles/PMC5618529/ /pubmed/28858211 http://dx.doi.org/10.3390/ijms18091880 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Min
Li, Dongyan
Tang, Yu
Wu, Fangxiang
Wang, Jianxin
CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title_full CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title_fullStr CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title_full_unstemmed CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title_short CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
title_sort cytocluster: a cytoscape plugin for cluster analysis and visualization of biological networks
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5618529/
https://www.ncbi.nlm.nih.gov/pubmed/28858211
http://dx.doi.org/10.3390/ijms18091880
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