title: Integration of biological networks and gene expression data using Cytoscape.
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.
authors.affiliation: Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.
authors.forename: Melissa S
authors.initials: MS
authors.lastname: Cline
authors.forename: Michael
authors.initials: M
authors.lastname: Smoot
authors.forename: Ethan
authors.initials: E
authors.lastname: Cerami
authors.forename: Allan
authors.initials: A
authors.lastname: Kuchinsky
authors.forename: Nerius
authors.initials: N
authors.lastname: Landys
authors.forename: Chris
authors.initials: C
authors.lastname: Workman
authors.forename: Rowan
authors.initials: R
authors.lastname: Christmas
authors.forename: Iliana
authors.initials: I
authors.lastname: Avila-Campilo
authors.forename: Michael
authors.initials: M
authors.lastname: Creech
authors.forename: Benjamin
authors.initials: B
authors.lastname: Gross
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.forename: Ruth
authors.initials: R
authors.lastname: Isserlin
authors.forename: Ryan
authors.initials: R
authors.lastname: Kelley
authors.forename: Sarah
authors.initials: S
authors.lastname: Killcoyne
authors.forename: Samad
authors.initials: S
authors.lastname: Lotia
authors.forename: Steven
authors.initials: S
authors.lastname: Maere
authors.forename: John
authors.initials: J
authors.lastname: Morris
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Ono
authors.forename: Vuk
authors.initials: V
authors.lastname: Pavlovic
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
authors.forename: Aditya
authors.initials: A
authors.lastname: Vailaya
authors.forename: Peng-Liang
authors.initials: PL
authors.lastname: Wang
authors.forename: Annette
authors.initials: A
authors.lastname: Adler
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Conklin
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Martin
authors.initials: M
authors.lastname: Kuiper
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Ilya
authors.initials: I
authors.lastname: Schmulevich
authors.forename: Benno
authors.initials: B
authors.lastname: Schwikowski
authors.forename: Guy J
authors.initials: GJ
authors.lastname: Warner
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D040901:Proteomics / Q000379:methods; D012333:RNA, Messenger / Q000378:metabolism*; D012984:Software
chemical_list: D012333:RNA, Messenger