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CytoCluster specifications

Information


Unique identifier OMICS_20754
Name CytoCluster
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 2.1.0
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Documentation


Maintainers


  • person_outline Fang-Xiang Wu
  • person_outline Min Li
  • person_outline Yu Tang
  • person_outline Dongyan Li

Publication for CytoCluster

CytoCluster citations

 (7)
library_books

Special Protein Molecules Computational Identification

2018
Int J Mol Sci
PMCID: 5855758
PMID: 29439426
DOI: 10.3390/ijms19020536

[…] in complexes []. Various plugins based on cytoscape, such as CytoNCA [], ClusterViz [], DyNetViewer [], CytoCtrlAnalyser [], were developed to analyze biological networks from different perspectives. CytoCluster [] in our special issue is a popular clustering tool which integrates six clustering algorithms and BinGO function. Since it was established in July 2013, CytoCluster has been downloaded m […]

library_books

Identification of novel diagnostic biomarkers for thyroid carcinoma

2017
Oncotarget
PMCID: 5762342
PMID: 29340074
DOI: 10.18632/oncotarget.22873

[…] and PCG. Co-expressed pairs were defined with a cutoff of |PCC| ≥ 0.7 and P < 0.001. Network interactions were graphed using Cytoscape software (version 3.2.1) []. Two sub-modules were identified by CytoCluster [], with the HC-PIN clustering algorithm and other parameters as default, which is a plugin in Cytoscape. […]

library_books

Functional annotation of Alzheimer's disease associated loci revealed by GWASs

2017
PLoS One
PMCID: 5484478
PMID: 28650998
DOI: 10.1371/journal.pone.0179677

[…] dicate the relevance of a protein as functionally capable of holding together communicating proteins. To select functional modules, a functional module analysis of the network was performed by way of CytoCluster plug-in in Cytoscape, with a score > 2.Hub proteins (genes) have higher node degrees and account for 20% of the total number of nodes. Bottleneck proteins are defined as proteins (genes) t […]

library_books

Identification of Pharmacologically Tractable Protein Complexes in Cancer Using the R Based Network Clustering and Visualization Program MCODER

2017
Biomed Res Int
PMCID: 5485287
PMID: 28691013
DOI: 10.1155/2017/1016305

[…] on Maximal Clique (CMC) [], ClusterMaker [], and Clustering with Overlapping Neighborhood Expansion (ClusterONE) []. Many of these algorithms have been implemented in various Cytoscape applications (CytoCluster, ClusterViz [], and ClusterMaker []), as well as in java-based applications (C-DEVA []). Of these, as of February 2017, MCODE was the most downloaded Cytoscape application within the clust […]

library_books

Co acclimation of bacterial communities under stresses of hydrocarbons with different structures

2016
Sci Rep
PMCID: 5048299
PMID: 27698451
DOI: 10.1038/srep34588

[…] th similar variation tendency which could be grouped together and create numerous “functional groups”. These functional groups could be separated from the whole network as “subnetworks” by executing “cytocluster” in the software of cytoscape. Combing predicated functions for each bacterial phylotype, these functional groups were annotated with different functions (). For example, two functional gr […]

library_books

Identification of Molecular Targets for Predicting Colon Adenocarcinoma

2016
PMCID: 4754092
PMID: 26868022
DOI: 10.12659/MSM.895881

[…] ing is an important means to identify functional modules, which not only helps understand the organizational structure of biological systems, but also contributes to predicting biomolecule functions. CytoCluster plugin can be used to identify gene clusters in the sub-network constructed by miRNA and its target gene (http://apps.cytoscape.org/apps/cytocluster). IPCA algorithm was used in cluster id […]


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CytoCluster institution(s)
School of Information Science and Engineering, Central South University, Changsha, China; School of software, Central South University, Changsha, China; Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
CytoCluster funding source(s)
Supported in part by the National Natural Science Foundation of China under Grants (No. 61622213, No. 61370024 and No. 61420106009).

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