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cyto-Hubba specifications

Information


Unique identifier OMICS_12244
Name cyto-Hubba
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.6
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Documentation


Maintainer


  • person_outline Ming-Tat Ko

Information


Unique identifier OMICS_12244
Name cyto-Hubba
Interface Web user interface
Restrictions to use None
Input data Tab, Data with weight value or PSI
Computer skills Basic
Stability Stable
Maintained Yes

Download


download.png

Documentation


Maintainer


  • person_outline Ming-Tat Ko

Publication for cyto-Hubba

cyto-Hubba citations

 (6)
library_books

Insights from the protein protein interaction network analysis of Mycobacterium tuberculosis toxin antitoxin systems

2017
Bioinformation
PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] Cyto-Hubba [], a java plugin for Cytoscape software, was employed to determine the hub proteins of PPI network of Mtb TA systems. In this study, two centrality measurements, i.e. betweenness and radia […]

library_books

Identification of Novel Pathways in Plant Lectin Induced Cancer Cell Apoptosis

2016
Int J Mol Sci
PMCID: 4783960
PMID: 26867193
DOI: 10.3390/ijms17020228

[…] edges per node, that is, the number of interacting partners. A node with high degree is called a network hub, which represents a protein with many interacting partner proteins [,]. Here, we used the cyto-Hubba (Hub Objects Analyzer; Taipei, Taiwan) plug-in to provide several topological analysis algorithms which included degree calculation for Cytoscape to explore important nodes/hubs in an inter […]

library_books

Exploring drug target interaction networks of illicit drugs

2013
BMC Genomics
PMCID: 3849475
PMID: 24268016
DOI: 10.1186/1471-2164-14-S4-S1

[…] v . To identify the bridge nodes based on the betweenness, we adopted the method above used to determine hubs. We first calculated the betweenness using algorithms implemented in the Cytoscape plugin cyto-Hubba (v. 1.6) [] and then drew the betweenness distribution to find the point that the distribution begins to reach its asymptote. The nodes, including drugs and genes, with a betweenness higher […]

library_books

Relaxation Response Induces Temporal Transcriptome Changes in Energy Metabolism, Insulin Secretion and Inflammatory Pathways

2013
PLoS One
PMCID: 3641112
PMID: 23650531
DOI: 10.1371/journal.pone.0062817

[…] lected. The interaction information was obtained using literature search, information from knowledge base databases such as MIPS, DIPS, HPRD and ingenuity systems , . Networks were analyzed using the cyto-Hubba plug-in for Cytoscape 2.8 platform to identify network hubs and bottlenecks, which may represent the key regulatory nodes in the network . The network consisting of the top 20 focus gene hu […]

library_books

Circulating miRNA profile in HCV infected serum: novel insight into pathogenesis

2013
Sci Rep
PMCID: 3615409
PMID: 23549102
DOI: 10.1038/srep01555

[…] ere retrieved from STRING, a database of known and predicted protein interactions. Networks were presented using Cytoscape and the hubs of networks were identified using a plug in of Cytoscape called cyto-Hubba. […]

library_books

Protein Interaction Network of Arabidopsis thaliana Female Gametophyte Development Identifies Novel Proteins and Relations

2012
PLoS One
PMCID: 3519845
PMID: 23239973
DOI: 10.1371/journal.pone.0049931

[…] Cyto-Hubba, as a hub finder/analyzer software, was used to find essential proteins/hubs . These essential proteins/hubs may serve as candidates of novel genes involved in FG development. The subnetwor […]


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cyto-Hubba institution(s)
Department of Computer Science and Information Engineering, Nanhua University, Chiayi County, Taiwan; Institute of Information Science, Academia Sinica, Taipei, Taiwan; Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taiwan; Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan; Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan; Research Center of Information Technology Innovation, Academia Sinica, Taipei, Taiwan
cyto-Hubba funding source(s)
Ministry of Science and Technology (MOST), Taiwan, for financially supporting this research through MOST 97-2221-E-008-048, MOST 100-2628-E-001 -007 -MY3 and MOST 103-2311-B-001 -033 -MY3, MOST 101-2321-B-001-043-MY2 and MOST 102-2811-B-001-046.

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