Integration of biological networks and gene expression data using Cytoscape

Publication: Research - peer-reviewJournal article – Annual report year: 2007

  • Author: Cline, M.S.

  • Author: Smoot, M.

  • Author: Cerami, E.

  • Author: Kuchinsky, A.

  • Author: Landys, N.

  • Author: Workman, Christopher

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Christmas, R.

  • Author: Avila-Campilo, I.

  • Author: Creech, M.

  • Author: Gross, B.

  • Author: Hanspers, K.

  • Author: Isserlin, R.

  • Author: Kelley, R.

  • Author: Killcoyne, S.

  • Author: Lotia, S.

  • Author: Maere, S.

  • Author: Morris, J.

  • Author: Ono, K.

  • Author: Pavlovic, V.

  • Author: Pico, A.R.

  • Author: Vailaya, A.

  • Author: Wang, P.L.

  • Author: Adler, A.

  • Author: Conklin, B.R.

  • Author: Hood, L.

  • Author: Kuiper, M.

  • Author: Sander, C.

  • Author: Schmulevich, I.

  • Author: Schwikowski, B.

  • Author: Warner, G.J.

  • Author: Ideker, T.

  • Author: Bader, G.D.

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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
StatePublished - 2007
CitationsWeb of Science® Times Cited: 800
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ID: 3874523