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Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Pubmed ID: 14597658


  • Shannon P
  • Markiel A
  • Ozier O
  • Baliga NS
  • Wang JT
  • Ramage D
  • Amin N
  • Schwikowski B
  • Ideker T


Genome research

Publication Data

November 4, 2003

Associated Grants

  • Agency: NIGMS NIH HHS, Id: P20 GM64361

Mesh Terms

  • Algorithms
  • Archaeal Proteins
  • Bacteriophage lambda
  • Computational Biology
  • Halobacterium
  • Internet
  • Models, Biological
  • Neural Networks (Computer)
  • Phenotype
  • Software
  • Software Design
  • Stochastic Processes