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Integration of biological networks and gene expression data using Cytoscape

Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, et al. (2007) NATURE PROTOCOLS. 2(10). p.2366-2382
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MOLECULAR INTERACTION DATABASE, YEAST SACCHAROMYCES-CEREVISIAE, PROTEIN-INTERACTION NETWORKS, MICROARRAY DATA, SYSTEMS BIOLOGY, PLUG-IN, PATHWAYS, VISUALIZATION, ONTOLOGY, RESOURCE
journal title
NATURE PROTOCOLS
Nat. Protoc.
volume
2
issue
10
pages
2366 - 2382
Web of Science type
Article
Web of Science id
000253139900010
JCR category
PHYSICS, MULTIDISCIPLINARY
JCR impact factor
14.677 (2007)
JCR rank
3/64 (2007)
JCR quartile
1 (2007)
ISSN
1745-2473
DOI
10.1038/nprot.2007.324
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
419347
handle
http://hdl.handle.net/1854/LU-419347
date created
2008-06-17 13:47:00
date last changed
2016-12-19 15:42:36
@article{419347,
  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.},
  author       = {Cline, Melissa S and Smoot, Michael and Cerami, Ethan and Kuchinsky, Allan and Landys, Nerius and Workman, Chris and Christmas, Rowan and Avila-Campilo, Iliana and Creech, Michael and Gross, Benjamin and Hanspers, Kristina and Isserlin, Ruth and Kelley, Ryan and Killcoyne, Sarah and Lotia, Samad and Maere, Steven and Morris, John and Ono, Keiichiro and Pavlovic, Vuk and Pico, Alexander R and Vailaya, Aditya and Wang, Peng-Liang and Adler, Annette and Conklin, Bruce R and Hood, Leroy and Kuiper, Martin and Sander, Chris and Schmulevich, Ilya and Schwikowski, Benno and Warner, Guy J and Ideker, Trey and Bader, Gary D},
  issn         = {1745-2473},
  journal      = {NATURE PROTOCOLS},
  keyword      = {MOLECULAR INTERACTION DATABASE,YEAST SACCHAROMYCES-CEREVISIAE,PROTEIN-INTERACTION NETWORKS,MICROARRAY DATA,SYSTEMS BIOLOGY,PLUG-IN,PATHWAYS,VISUALIZATION,ONTOLOGY,RESOURCE},
  language     = {eng},
  number       = {10},
  pages        = {2366--2382},
  title        = {Integration of biological networks and gene expression data using Cytoscape},
  url          = {http://dx.doi.org/10.1038/nprot.2007.324},
  volume       = {2},
  year         = {2007},
}

Chicago
Cline, Melissa S, Michael Smoot, Ethan Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, et al. 2007. “Integration of Biological Networks and Gene Expression Data Using Cytoscape.” Nature Protocols 2 (10): 2366–2382.
APA
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., et al. (2007). Integration of biological networks and gene expression data using Cytoscape. NATURE PROTOCOLS, 2(10), 2366–2382.
Vancouver
1.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, et al. Integration of biological networks and gene expression data using Cytoscape. NATURE PROTOCOLS. 2007;2(10):2366–82.
MLA
Cline, Melissa S, Michael Smoot, Ethan Cerami, et al. “Integration of Biological Networks and Gene Expression Data Using Cytoscape.” NATURE PROTOCOLS 2.10 (2007): 2366–2382. Print.