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PMID: 17947979 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Integration of biological networks and gene expression data using Cytoscape.

Nature protocols ·Vol. 2 ·No. 10 ·2007-00-00 ·Pages 2366-82

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 PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD

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.

MeSH Terms
Computational Biology/methods Gene Expression Profiling/methods Gene Regulatory Networks Genomics/methods Proteomics/methods RNA, Messenger/metabolism Software
Chemicals
RNA, Messenger
Authors & Affiliations
32 authors, click to expand affiliations / ORCID
Cline Melissa S
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.
Smoot Michael
Cerami Ethan
Kuchinsky Allan
Landys Nerius
Workman Chris
Christmas Rowan
Avila-Campilo Iliana
Creech Michael
Gross Benjamin
Hanspers Kristina
Isserlin Ruth
Kelley Ryan
Killcoyne Sarah
Lotia Samad
Maere Steven
Morris John
Ono Keiichiro
Pavlovic Vuk
Pico Alexander R
Vailaya Aditya
Wang Peng-Liang
Adler Annette
Conklin Bruce R
Hood Leroy
Kuiper Martin
Sander Chris
Schmulevich Ilya
Schwikowski Benno
Warner Guy J
Ideker Trey
Bader Gary D
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Article Info
Journal
Nature protocols
Abbr.
Nat Protoc
ISSN
1750-2799
DOI
10.1038/nprot.2007.324
Published
2007-00-00
Pages
2366-82
Language
English
Region
England
NLM ID
101284307
PMCID
PMC3685583
Subset
IM
Grants
NIGMS NIH HHS · R01 GM070743-03 · United States
NIGMS NIH HHS · R01 GM070743-04 · United States
NIGMS NIH HHS · R01 GM070743-03S1 · United States
NIGMS NIH HHS · R01 GM070743-05 · United States
NIGMS NIH HHS · R01 GM070743-01 · United States
NIGMS NIH HHS · R01 GM070743 · United States
NIGMS NIH HHS · GM070743-01 · United States
NIGMS NIH HHS · R01 GM070743-02 · United States
External Links
PubMed source DOI: 10.1038/nprot.2007.324 PMC Full Text View journal details
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