Integration of biological networks and gene expression data using Cytoscape

M.S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, Christopher Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, K. Hanspers, R. Isserlin, R. Kelley, S. Killcoyne, S. Lotia, S. Maere, J. Morris, K. Ono, V. Pavlovic, A.R. PicoA. Vailaya, P.L. Wang, A. Adler, B.R. Conklin, L. Hood, M. Kuiper, C. Sander, I. Schmulevich, B. Schwikowski, G.J. Warner, T. Ideker, G.D. Bader

    Research output: Contribution to journalJournal articleResearchpeer-review


    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.
    Original languageEnglish
    JournalNature Protocols
    Issue number10
    Pages (from-to)2366-2382
    Publication statusPublished - 2007

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