Integration of biological networks and gene expression data using Cytoscape.

TitleIntegration of biological networks and gene expression data using Cytoscape.
Publication TypeJournal Article
Year of Publication2007
AuthorsCline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang P-L, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
JournalNat Protoc
Volume2
Issue10
Pagination2366-82
Date Published2007
ISSN1750-2799
KeywordsComputational Biology, Gene Expression Profiling, Gene Regulatory Networks, Genomics, Proteomics, RNA, Messenger, Software
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.

DOI10.1038/nprot.2007.324
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/17947979?dopt=Abstract
PMCPMC3685583
Alternate JournalNat Protoc
PubMed ID17947979