Integration of biological networks and gene expression data using Cytoscape.

@article{citeulike:1838523, 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.}, address = {Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.}, author = {Cline, M. S. and Smoot, M. and Cerami, E. and Kuchinsky, A. and Landys, N. and Workman, C. and Christmas, R. and Avila-Campilo, I. and Creech, M. and Gross, B. and Hanspers, K. and Isserlin, R. and Kelley, R. and Killcoyne, S. and Lotia, S. and Maere, S. and Morris, J. and Ono, K. and Pavlovic, V. and Pico, A. R. and Vailaya, A. and Wang, P. L. and Adler, A. and Conklin, B. R. and Hood, L. and Kuiper, M. and Sander, C. and Schmulevich, I. and Schwikowski, B. and Warner, G. J. and Ideker, T. and Bader, G. D. }, citeulike-article-id = {1838523}, doi = {http://dx.doi.org/10.1038/nprot.2007.324}, issn = {1750-2799}, journal = {Nat Protoc}, keywords = {integration, network, software}, number = {10}, pages = {2366--2382}, posted-at = {2008-01-09 11:46:14}, priority = {0}, 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} }

TY - JOUR ID - citeulike:1838523 L3 - citeulike-article-id:1838523 TI - Integration of biological networks and gene expression data using Cytoscape. JF - Nat Protoc VL - 2 IS - 10 SP - 2366 EP - 2382 AD - Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France. SN - 1750-2799 N2 - 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. KW - integration KW - network KW - software AU - Cline, MS AU - Smoot, M AU - Cerami, E AU - Kuchinsky, A AU - Landys, N AU - Workman, C AU - Christmas, R AU - Avila-Campilo, I AU - Creech, M AU - Gross, B AU - Hanspers, K AU - Isserlin, R AU - Kelley, R AU - Killcoyne, S AU - Lotia, S AU - Maere, S AU - Morris, J AU - Ono, K AU - Pavlovic, V AU - Pico, AR AU - Vailaya, A AU - Wang, PL AU - Adler, A AU - Conklin, BR AU - Hood, L AU - Kuiper, M AU - Sander, C AU - Schmulevich, I AU - Schwikowski, B AU - Warner, GJ AU - Ideker, T AU - Bader, GD PY - 2007/// UR - http://dx.doi.org/10.1038/nprot.2007.324 ER -