Cytoscape: a software environment for integrated models of biomolecular interaction networks
- PMID: 14597658
- PMCID: PMC403769
- DOI: 10.1101/gr.1239303
Cytoscape: a software environment for integrated models of biomolecular interaction networks
Abstract
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.
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WEB SITE REFERENCES
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- http://biodata.mshri.on.ca/; Osprey Network Visualization System
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- http://pim.hybrigenics.com/; PIMRider
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- http://predictome.bu.edu/; Predictome Project
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- http://www.cytoscape.org/; Cytoscape v1.1 Home Page
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