Cytoscape.org

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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.