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

Genome Res. 2003 Nov;13(11):2498-504. doi: 10.1101/gr.1239303.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / metabolism
  • Bacteriophage lambda / physiology
  • Computational Biology / methods*
  • Halobacterium / chemistry
  • Halobacterium / cytology
  • Halobacterium / physiology
  • Internet
  • Models, Biological*
  • Neural Networks, Computer*
  • Phenotype
  • Software / trends*
  • Software Design*
  • Stochastic Processes


  • Archaeal Proteins