title: Exploring biological networks with Cytoscape software.
abstract: Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determine and analyze the interconnectivity of a list of genes or proteins. This unit explains how to use Cytoscape to load and navigate biological network information and view mRNA expression profiles and other functional genomics and proteomics data in the context of the network obtained for genes of interest. Additional analyses that can be performed with Cytoscape are also discussed.
authors.affiliation: University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.
authors.forename: Natalie
authors.initials: N
authors.lastname: Yeung
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California.
authors.forename: Melissa S
authors.initials: MS
authors.lastname: Cline
authors.affiliation: Agilent Technologies, Santa Clara, California.
authors.forename: Allan
authors.initials: A
authors.lastname: Kuchinsky
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, California.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Smoot
authors.affiliation: University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
mesh_terms: D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D003628:Database Management Systems / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D006801:Humans; D040901:Proteomics / Q000379:methods; D021281:Quantitative Structure-Activity Relationship; D012984:Software