Displaying Chemical Information on a Biological Network Using Cytoscape
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.
Key wordsCytoscape Network visualization Druggable targets Chemical biological networks Chemical networks
The second protocol discussed here is inspired by and adapted from a presentation by Anna Gaulton at the “Small molecule bioactivity resources at the EBI” course in January 2010. This work was supported by grants from the NHGRI to CN and GG, the CIHR to CN (MOPS-84305) and to GG (MOPS-81340), by NSERC support to GB and IMW, and from a Marie Curie fellowship to IMW. GG is a Canada Research Chair in Chemical Biology.
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