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. 2008 Sep:Chapter 8:8.13.1-8.13.20.
doi: 10.1002/0471250953.bi0813s23.

Exploring biological networks with Cytoscape software

Natalie Yeung  1 , Melissa S Cline  2 , Allan Kuchinsky  3 , Michael E Smoot  4 , Gary D Bader  1
Affiliations

Exploring biological networks with Cytoscape software

Natalie Yeung et al. Curr Protoc Bioinformatics. 2008 Sep.

Abstract

Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determine and analyze the interconnectivity of a list of genes or proteins. This unit explains how to use Cytoscape to load and navigate biological network information and view mRNA expression profiles and other functional genomics and proteomics data in the context of the network obtained for genes of interest. Additional analyses that can be performed with Cytoscape are also discussed.

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References

Literature Cited

References
    1. Bader, G.D. and Hogue, C.W. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2 (http://www.biomedcentral.com/1471-2105/4/2).
    1. Bader, G. , Donaldson, I. , Wolting, C. , Ouellette, B. , Pawson, T. , and Hogue, C. 2001. BIND-The Biomolecular Interaction Network Database. Nucleic Acids Res. 29: 242-245.
    1. Bader, G.D. , Cary, M.P. , and Sander, C. 2006. Pathguide: A pathway resource list. Nucleic Acids Res. 34: D504- D506.
    1. Cerami, E.G. , Bader, G.D. , Gross, B.E. , and Sander, C. 2006. cPath: Open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 7: 497 (http://www.biomedcentral.com/1471-2105/7/497).
    1. Christie, K.R. , Weng, S. , Balakrishnan, R. , Costanzo, M.C. , Dolinski, K. , Dwight, S.S. , Engel, S.R. , Feierbach, B. , Fisk, D.G. , Hirschman, J.E. , Hong, E.L. , Issel-Tarver, L. , Nash, R. , Sethuraman, A. , Starr, B. , Theesfeld, C.L. , Andrada, R. , Binkley, G. , Dong, Q. , Lane, C. , Schroeder, M. , Botstein, D. , and Cherry, J.M. 2004. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32: D311-D314.
Key References
    1. Bader et al., 2006. See above.
    1. Shannon et al., 2003. See above.
Internet Resources
    1. http://www.cytoscape.org
    1. http://java.sun.com
    1. http://www.yeastgenome.org
    1. http://www.reactome.org
    1. http://llama.med.harvard.edu/cgi/synergizer/translate

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