Protocol abstract
Nature Protocols 2, - 2366 - 2382 (2007)
Published online: 27 September 2007 | doi:10.1038/nprot.2007.324
Subject Category: Computational and theoretical biology
Integration of biological networks and gene expression data using Cytoscape
Melissa S Cline1,2, Michael Smoot3, Ethan Cerami4, Allan Kuchinsky5, Nerius Landys3, Chris Workman6, Rowan Christmas7, Iliana Avila-Campilo7,8, Michael Creech9, Benjamin Gross4, Kristina Hanspers10, Ruth Isserlin11,12, Ryan Kelley3, Sarah Killcoyne7, Samad Lotia3, Steven Maere13,14, John Morris15, Keiichiro Ono3, Vuk Pavlovic11,12, Alexander R Pico10, Aditya Vailaya5,16, Peng-Liang Wang3, Annette Adler5, Bruce R Conklin10, Leroy Hood7, Martin Kuiper13,14, Chris Sander4, Ilya Schmulevich7, Benno Schwikowski1, Guy J Warner17, Trey Ideker3 & Gary D Bader11,12
Abstract
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.
- Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA.
- Department of Bioengineering, 9500 Gilman Drive, Mail Code 0412, La Jolla, California 92093-0412, USA.
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, New York 10021, USA.
- Agilent Laboratories, 3500 Deer Creek Road, MS 26U-16, Palo Alto, California 94304, USA.
- BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.
- The Institute for Systems Biology, Seattle, Washington 98103, USA.
- Rosetta Inpharmatics LLC, Merck & Co. Inc., 401 Terry Ave N, Seattle, Washington 98109, USA.
- Blue Oak Software, 1734 Austin Ave, Los Altos, California 94024-6103, USA.
- Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, California 94158, USA.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1.
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6.
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.
- Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
- Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2250, USA.
- Retrevo Inc., 440 N Wolfe Road, Sunnyvale, California 94085, USA.
- Unilever Safety and Environmental Assurance Centre, Colworth Park, Sharnbrook, Bedfordshire MK44 1LQ, UK.
Correspondence to: Trey Ideker3 e-mail: trey@bioeng.ucsd.edu
