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Integration of biological networks and gene expression data using Cytoscape.

Nature protocols

Software, Computational Biology, methods, Gene Expression Profiling, Gene Regulatory Networks, Genomics, Proteomics, RNA, Messenger, metabolism

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      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.

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      Journal
      10.1038/nprot.2007.324
      3685583
      17947979

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