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Cytoscape.org
Cytoscape is a freely-available bioinformatics software platform for
visualizing biological networks (e.g. molecular interaction networks) and
analyzing networks with gene expression profiles and other state data.
Core Features
• Customize network
data display using
visual styles
• Powerful graph
layout tools
• Easily organize
multiple networks
• Easily navigate
large networks
• Filter the network
• Plugin API
Input/Output
• Protein protein
interactions from BIND,
TRANSFAC databases
• Gene functional
annotations from Gene
Ontology (GO) and
KEGG databases
• Biological models from
Systems Biology Markup
Language (SBML)
• cPath: Cancer Pathway
database
• Proteomics Standards
Initiative Molecular
Interaction (PSI-MI) or
Biopathway Exchange
Language (BioPAX)
formats
• Oracle Spatial Network
data model
Additional features are available as plugins.
• jActiveModules: identify significant “active” subnetworks
• Expression Correlation Network: cluster expression data
• Agilent Literature Search: build networks by extracting
interactions from scientific literature.
• MCODE: finds clusters of highly interconnected regions in
networks
• cPath: query, retrieve and visualize interactions from the
MSKCC Cancer Pathway database
• BiNGO: determine which Gene Ontology (GO) categories are
statistically over-represented in a set of genes
• Motif Finder: runs a Gibbs sampling motif detector on
sequences for nodes in a Cytoscape network.
• CytoTalk: Interact with Cytoscape from Perl, Python, R, shell
scripts or C or C++ programs.