Integration of biological networks and gene expression data using Cytoscape

被引：1908

作者：

Cline, Melissa S. ^{[2
,3
]}

Smoot, Michael ^{[1
]}

Cerami, Ethan ^{[4
]}

Kuchinsky, Allan ^{[5
]}

Landys, Nerius ^{[1
]}

Workman, Chris ^{[6
]}

Christmas, Rowan ^{[7
]}

Avila-Campilo, Iliana ^{[7
,8
]}

Creech, Michael ^{[9
]}

Gross, Benjamin ^{[4
]}

Hanspers, Kristina ^{[10
]}

Isserlin, Ruth ^{[11
,12
]}

Kelley, Ryan ^{[1
]}

Killcoyne, Sarah ^{[7
]}

Lotia, Samad ^{[1
]}

Maere, Steven ^{[13
,14
]}

Morris, John ^{[15
]}

Ono, Keiichiro ^{[1
]}

Pavlovic, Vuk ^{[11
,12
]}

Pico, Alexander R. ^{[10
]}

Vailaya, Aditya ^{[5
,16
]}

Wang, Peng-Liang ^{[1
]}

Adler, Annette ^{[5
]}

Conklin, Bruce R. ^{[10
]}

Hood, Leroy ^{[7
]}

Kuiper, Martin ^{[13
,14
]}

Sander, Chris ^{[4
]}

Schmulevich, Ilya ^{[7
]}

Schwikowski, Benno ^{[2
]}

Warner, Guy J. ^{[17
]}

Ideker, Trey ^{[1
]}

Bader, Gary D. ^{[11
,12
]}

机构：

[1] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[2] Inst Pasteur, F-75724 Paris 15, France

[3] Univ Calif Santa Cruz, Dept Mol Cell & Dev Biol, Santa Cruz, CA 95064 USA

[4] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10021 USA

[5] Agilent Labs, Palo Alto, CA 94304 USA

[6] Tech Univ Denmark, BioCentrum DTU, DK-2800 Lyngby, Denmark

[7] Inst Syst Biol, Seattle, WA 98103 USA

[8] Rosetta Inpharmat LLC, Merck & Co Inc, Seattle, WA 98109 USA

[9] Blue Oak Software, Los Altos, CA 94024 USA

[10] Gladstone Inst Cardiovasc Dis, San Francisco, CA 94158 USA

[11] Univ Toronto, Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 3E1, Canada

[12] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5G 1L6, Canada

[13] VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium

[14] Univ Ghent, Dept Mol Genet, B-9052 Ghent, Belgium

[15] Univ Calif San Francisco, Dept Biopharmaceut Sci, San Francisco, CA 94143 USA

[16] Retrevo Inc, Sunnyvale, CA 94085 USA

[17] Unilever Safety & Environm Assurance Ctr, Sharnbrook MK44 1LQ, Beds, England

来源：

NATURE PROTOCOLS | 2007年 / 2卷 / 10期

关键词：

D O I：

10.1038/nprot.2007.324

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

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.

引用

页码：2366 / 2382

页数：17

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