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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

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Cytoscape.org

Cytoscape is a freely-available bioinformatics software platform forvisualizing biological networks (e.g. molecular interaction networks) andanalyzing 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.