Cytoscape specifications


Unique identifier OMICS_04119
Name Cytoscape
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.6.1
Stability Stable
Maintained Yes


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  • person_outline Trey Ideker <>

Cytoscape article

Cytoscape citations

PMCID: 5849708

[…] if any differentially expressed genes were significantly enriched in kegg pathways. to determine which gene ontology (go) categories were statistically overrepresented among the degs, topgo and cytoscape version 3.4.0 with bingo plugin version 3.0.3 (maere et al. 2005) were used to identify significantly enriched biological networks and to output the results as graphs., real time […]

PMCID: 5928633

[…] templates for dna sequencing., the gene ontology (go) enrichment analysis and the network visualization of the biological functions related to the differentially expressed genes were performed using cytoscape software with associated plug-ins (13). to create a functional network by selecting the cluego: function, go: biological process, all the network evidence and only the terms with various […]

PMCID: 5870351

[…] in module function. unknown genes were also annotated., the biggest gene co-expression network to date has been constructed (figure 1). the top 2000 highly connected probe pairs were visualized by cytoscape. the highest connected gene within the whole network is probe 1761661_s_at, which is annotated as an intergenic region; however, it localizes within the putative adhesin gene ycgv […]

PMCID: 5830583

[…] the enrichment in certain functional categories as defined by the go classification59. the gene set enrichment (gse) analysis was carried out using a combination of the bingo tool60 and the cytoscape software for visualization61. the enrichment test identifies the most abundant go terms in the sub-network compared to all the possible terms present in the complete annotation, using […]

PMCID: 5852588

[…] ranked genes in every module are thought to be hub genes. in order to identify the high degree genes which play a critical role in the protein-protein network (ppi), the cytohubba plugin based on cytoscape was used to perform the network analysis [19], and the high degree genes were identified., publicly available data and tools were employed to perform the survival analysis using […]

Cytoscape institution(s)
Institute for Systems Biology, Seattle, WA, USA

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