Category Cross-Omics>Pathway Analysis/Tools

Abstract Cytoscape is an open-source bioinformatics software platform that enables researchers to form a visual map of complex biological networks increasing their understanding of molecular pathways and the biological causes of disease. Cytoscape allows you to visualize molecular interaction networks and integrates these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.

Cytoscape supports the following features/capabilities:

Input --

Visualization --

Analysis --

Plugins that are available for network and molecular profile analysis. For example:

1) Filter the network to select subsets of nodes and/or interactions based on the current data. For instance, users may select nodes involved in a threshold number of interactions, nodes that share a particular GO annotation, or nodes whose gene expression levels change significantly in one or more conditions according to p-values loaded with the gene expression data.

2) Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of interactions, i.e. interaction subnetworks, whose genes show particularly high levels of differential expression. The interactions contained in each subnetwork provide hypotheses for the regulatory and signaling interactions in control of the observed expression changes.

3) Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families.

More info about Plugins --

Cytoscape includes a flexible Plugin architecture that enables developers to add extra functionality beyond that provided in the core. Plugins also provide a convenient place for testing out new Cytoscape features.

Current plugins are categorized into five (5) sections:

System Requirements

Cytoscape is a Java application (Java SE 5 or 6 only) verified to run on Linux, Windows, and Mac OS X. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform.

The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate.

Small NetworkVisualization

Large Network Analysis/Visualization


The Cytoscape project is an ongoing collaboration between:

Manufacturer Web Site Cytoscape project

Price Freely available for download from as an open source Java application.

G6G Abstract Number 20092

G6G Manufacturer Number 100709