Abstract
Cytoscape is a general network visualization, data integration, and analysis software package. Its development and use has been focused on the modeling requirements of systems biology, though it has been used in other fields. Cytoscape’s flexibility has encouraged many users to adopt it and adapt it to their own research by using the plugin framework offered to specialize data analysis, data integration, or visualization. Plugins represent collections of community-contributed functionality and can be used to dynamically extend Cytoscape functionality. This community of users and developers has worked together since Cytoscape’s initial release to improve the basic project through contributions to the core code and public offerings of plugin modules.
This chapter discusses what Cytoscape does, why it was developed, and the extensions numerous groups have made available to the public. It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Vladimir B and Andrej M. PAJEK – Program for large network analysis. Connections, 1998, 21:47–57.
Akira F, Mineo M, Hiroaki K, and Naoki T. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico, 2003, 1(5):159–162.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang J, Ramage D, Amin N, Schwikowski B, and Ideker T. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 2003, 13:2498–2504.
Smith J, Sydorskyy Y, Marelli M, Hwang D, Balouri H, Rachubinski R, and Aitchison J. Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Molecular Systems Biology, 2006, 2:2006.0009. http://www.nature.com/msb/journal/v2/n1/full/msb4100051.html
Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, and Galitski T. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Research, 2004, 14(3):380–390.
Forster J, Famili I, Fu P, Palsson BO, and Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research, 2003, 3(2):244–253.
Maere S, Heymans K, and Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics, 2005, 21(16):3448–3449.
Barsky A, Gardy JL, Hancock REW, and Munzner T. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 2007, 23(8): 1040–1042.
Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, and Galitski T. Derivation of genetic interaction networks from quantitative phenotype data. Genome Biology, 2005, 6(4):R38. http://genomebiology.com/2005/6/4/R38
Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, and Galitski T. Derivation of genetic interaction networks from quantitative phenotype data. Genome Biology, 2005, 6(4):R38. http://genomebiology.com/2005/6/4/R38
Barsky A, Gardy J, Hancock R, and Munzner T. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 2007, 23(8):1040–1042.
Vailaya A, Bluvas P, Kincaid R, Kuchinsky A, Creech M, and Adler A. An architecture for biological information extraction and representation. Bioinformatics, 2005, 21(4):430–438.
Ideker T, Ozier O, Schwikowski B, and Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 2002, 18(90001):S233–S240.
Taylor RJ, Siegel AF, and Galtiski T. Network motif analysis of a mutli-mode genetic network. Genome Biology, 2007, 8(8):R160. http://genomebiology.com/2007/8/8/R160
Acknowledgements
1. The project described was supported by grant number P50GMO76547 from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIMGS or the NIH.
2. Gregory W. Carter is supported by grant K25GM079404 from the National Institute of General Medical Sciences.
3. Funding for Cytoscape is provided by a federal grant from the US National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01 and the US National Science Foundation (NSF). Corporate funding is provided through a contract from Unilever PLC.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Killcoyne, S., Carter, G.W., Smith, J., Boyle, J. (2009). Cytoscape: A Community-Based Framework for Network Modeling. In: Nikolsky, Y., Bryant, J. (eds) Protein Networks and Pathway Analysis. Methods in Molecular Biology, vol 563. Humana Press. https://doi.org/10.1007/978-1-60761-175-2_12
Download citation
DOI: https://doi.org/10.1007/978-1-60761-175-2_12
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-174-5
Online ISBN: 978-1-60761-175-2
eBook Packages: Springer Protocols