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Integration of biological networks and gene expression data using Cytoscape

热1 xbinbzy 添加于 2010-10-20 15:45 | 3481 次阅读 | 0 个评论

作者
Cline 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
摘要
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.
详细资料
- 关键词: Computational Biology/*methods; Gene Expression Profiling/*methods; *Gene Regulatory Networks; Genomics/methods; Proteomics/methods; RNA, Messenger/*metabolism; *Software
- 文献种类:期刊
- 期刊名称: Nature Protocols
- 期刊缩写: Nat Protoc
- 期卷页: 2007年第2卷第10期 2366-2382页
- 地址: Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
- ISBN: 1750-2799
- 备注:PMID:17947979
相关链接 DOI URL