Integration of biological networks and gene expression data using Cytoscape.
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.
Cline
Melissa S
MS
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France.
Smoot
Michael
M
Cerami
Ethan
E
Kuchinsky
Allan
A
Landys
Nerius
N
Workman
Chris
C
Christmas
Rowan
R
Avila-Campilo
Iliana
I
Creech
Michael
M
Gross
Benjamin
B
Hanspers
Kristina
K
Isserlin
Ruth
R
Kelley
Ryan
R
Killcoyne
Sarah
S
Lotia
Samad
S
Maere
Steven
S
Morris
John
J
Ono
Keiichiro
K
Pavlovic
Vuk
V
Pico
Alexander R
AR
Vailaya
Aditya
A
Wang
Peng-Liang
PL
Adler
Annette
A
Conklin
Bruce R
BR
Hood
Leroy
L
Kuiper
Martin
M
Sander
Chris
C
Schmulevich
Ilya
I
Schwikowski
Benno
B
Warner
Guy J
GJ
Ideker
Trey
T
Bader
Gary D
GD
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
D012333:RNA, Messenger