Cytoscape protocols

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chevron_left Protein-protein interaction prediction Network visualization Figure creation Differential co-expression analysis chevron_right
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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 <>

Publication for Cytoscape

Cytoscape in pipelines

PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] genes with fold changes > 1.5 and a benjamini-hochberg corrected p value < 0.05 (default parameter used in the cuffdiff algorithm) were considered to be differentially expressed., we used the cytoscape plugin cluego [] (together with the go annotation (goa embl-ebi) ( released on 11/17/2016. the background set for go was all genes with annotated go entries […]

PMCID: 5753908
PMID: 29291611
DOI: 10.5056/jnm17021

[…] the selected 1564 features were then mapped to genes, and the list of 858 unique genes were subjected to ontology/pathway analysis and visualized by using the “cluego” and “reactomefi” packages in cytoscape, from which enriched terms with p-value < 0.05 were identified., dnase-treated total rna (1 μg) was reverse-transcribed via an iscript cdna synthesis kit (bio-rad) to prepare 20 μl […]

PMCID: 5755453
PMID: 29301495
DOI: 10.1186/s12865-017-0238-4

[…] their default settings., in each module, a transcript was considered as an intra-modular hub node if its connectivity was equal or more than 90% of the most connected node., cluego [], a widely used cytoscape plugin, was used to identify potential biological interpretation of functional modules in the network. the latest updates of gene ontology annotation database (goa) [] and reactome pathway […]

PMCID: 5765694
PMID: 29325581
DOI: 10.1186/s40168-017-0395-y

[…] the average over 10 trials. figures resulting from qiime clustering analyses were generated using the interactive tree of life (itol) tool []. for visualization of the differential microbiome, cytoscape software version 3.1.3 was used []., for the microbiota data, statistical significance between contrasts with regard to taxonomy abundances was tested by a non-parametric (unpaired) […]

PMCID: 5773548
PMID: 29348603
DOI: 10.1038/s41598-018-19424-9

[…] was detected with ecl system., network analysis was performed using string database, minimal interactions score was set to “high confidence”. string generated networks were further analyzed by cytoscape., proteins were considered as orthologues when the blastp e-value was smaller than 1 × 10−10 and over 80% of residues in both sequences included in the blastp alignment. enrichment analysis […]

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Cytoscape in publications

PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w

[…] gene set (n = 403), we also utilized ipa to perform the “upstream regulator analysis” (ura) to identify which were the most significant upstream regulators inside this gene network. we utilized the cytoscape software for the network visualization of ipa results. finally, the sub-cellular and extra-cellular ‘locations’ of the genes shown in the ura graph were assigned using ipa software., […]

PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] proteins present in at least one complex were used as the background population. p-values were corrected for multiple testing as explained above. protein interaction networks were visualized using cytoscape and gephi. detailed information about all 960 identified interactors of mll-fusion proteins is provided in supplementary data ., molm-13 cells transduced with mini-pools of retroviral […]

PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] regions using pwmenrich r package. tfs, for which expression was negatively or positively correlated to the basal-classical component, were regarded as classical or basal tfs, respectively. cytoscape was used for network visualization and the cluego app was applied to target genes for clustered enriched pathway network representation., cells (3e5) were plated in six-well plates and 24 h […]

PMCID: 5958082
PMID: 29773851
DOI: 10.1038/s41598-018-26163-4

[…] the combinational regulation of mirna and tf in each cluster. the networks were created by joining in each cluster mirnas and tfs with the enriched target genes as well as interacting proteins using cytoscape. if there was more than one mirna from the same functional family (e.g. mir-300 and mir-381), only one was used in network construction. figure  shows networks from 5 clusters, […]

PMCID: 5955976
PMID: 29769534
DOI: 10.1038/s41598-018-22493-5

[…] renal carcinoma. in addition, to provide a readable graphic representation of the complex relationship between target genes and relative kegg pathway, the “pathway-gene network” was constructed by cytoscape (fig. ).figure 4figure 5, the string (a database of known and predicted protein interactions) and cytoscape were used to predict protein interactions among the target genes of five-mirna […]

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

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