Cytoscape Web statistics

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Cytoscape Web specifications


Unique identifier OMICS_17522
Name Cytoscape Web
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes



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  • person_outline Gary Bader <>

Additional information

Tuto:; This project has been replaced by Cytoscape.js, and is no longer active.

Publication for Cytoscape Web

Cytoscape Web in pipeline

PMCID: 4079066
PMID: 25071821
DOI: 10.3389/fgene.2014.00191

[…] applied to study osmoregulation in synechococcus sp. wh8102 (mao et al., ). networks can be validated with gene expression data (provided by the user), and can be visualized and explored using the cytoscape web interface (lopes et al., ). one of its main advantages is that networks can be exported as images in various formats or as xml-based formats, i.e., svg and xgmml., finally, fame […]

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Cytoscape Web in publications

PMCID: 5779940
PMID: 29039500
DOI: 10.3892/mmr.2017.7741

[…] at different hierarchical levels and the hsapiens_module_922 was the most enriched hierarchical network module. to reveal associations among genes within the most enriched network module, the cytoscape web plug in was used to visualize in a network graph the input genes (in green) and their direct neighbors (in white). as demonstrated in , interferon-induced protein with tetratricopeptide […]

PMCID: 5430665
PMID: 28450740
DOI: 10.1038/s41598-017-01156-x

[…] uncertainty and multifactorial design. in this test the error due to multiple testing is controlled through the priors and hence this control is embedded in the overall procedure., netview and cytoscape web-based platforms were used to analyse the putative targets. netview ( collects co-expression information for human and murine transcripts. we queried the netview network […]

PMCID: 5397463
PMID: 28473844
DOI: 10.3389/fpls.2017.00618

[…] coefficients (pccs) and mutual rank (mr) for gene co-expression () were used to construct the gmelf4 network. a table including the top 50 genes with the greatest mr values was constructed. the cytoscape web software program version 3.4.0 () was used to display the gmelf4 (central node) and all its co-expression genes, sorted according to mr values., in this study, the soybean elf4 […]

PMCID: 5376343
PMID: 28306714
DOI: 10.1371/journal.pcbi.1005432

[…] directly to them or through one or several groups. such groups are “exploded” before the path search step described below., cytoscape 3.4 ( was used to generate figures and cytoscape web was used to provide interactive access to the syk network., we searched for “near-shortest paths” between syk and a list of targets, using an approach similar to the classical dijkstra […]

PMCID: 5737374
PMID: 28338930
DOI: 10.1093/dnares/dsx009

[…] is identifying the correlation network of a group of query genes. the algorithm of the correlation coefficient and cut-off value should be set first. the correlation networks are constructed by cytoscape web based on the setting parameters ()., enrichment analysis helps researchers to find the important pathways or functional go terms from a group of query genes. to determine […]

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Cytoscape Web institution(s)
Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
Cytoscape Web funding source(s)
Supported by Genome Canada through the Ontario Genomics Institute (grant number 2007-OGI-TD-05); the U.S. National Institute of General Medical Sciences of the National Institutes of Health (grant number 2R01GM070743-06).

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