title: Displaying chemical information on a biological network using Cytoscape.
abstract: Cytoscape is an open-source software package that is widely used to integrate and visualize diverse data sets in biology. This chapter explains how to use Cytoscape to integrate open-source chemical information with a biological network. By visualizing information about known compound-target interactions in the context of a biological network of interest, one can rapidly identify novel avenues to perturb the system with compounds and, for example, potentially identify therapeutically relevant targets. Herein, two different protocols are explained in detail, with no prior knowledge of Cytoscape assumed, which demonstrate how to incorporate data from the ChEMBL database with either a gene-gene or a protein-protein interaction network. ChEMBL is a very large, open-source repository of compound-target information available from the European Molecular Biology Laboratory.
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
authors.forename: Iain M
authors.initials: IM
authors.lastname: Wallace
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Guri
authors.initials: G
authors.lastname: Giaever
authors.forename: Corey
authors.initials: C
authors.lastname: Nislow
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D030562:Databases, Protein; D053263:Gene Regulatory Networks / Q000187:drug effects*; D058990:Molecular Targeted Therapy; D060066:Protein Interaction Maps / Q000187:drug effects*; D012984:Software