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Int. J. Mol. Sci. 2017, 18(9), 1880; doi:10.3390/ijms18091880

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

1
School of Information Science and Engineering, Central South University, Changsha 410083, China
2
School of software, Central South University, Changsha 410083, China
3
Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
*
Author to whom correspondence should be addressed.
Received: 7 August 2017 / Revised: 22 August 2017 / Accepted: 23 August 2017 / Published: 31 August 2017
(This article belongs to the Special Issue Special Protein Molecules Computational Identification)
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Abstract

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. View Full-Text
Keywords: biological networks; cluster analysis; cytoscape; visualization biological networks; cluster analysis; cytoscape; visualization
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Li, M.; Li, D.; Tang, Y.; Wu, F.; Wang, J. CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks. Int. J. Mol. Sci. 2017, 18, 1880.

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