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Displaying Chemical Information on a Biological Network Using Cytoscape

  • Iain M. Wallace
  • Gary D. Bader
  • Guri Giaever
  • Corey NislowEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 781)

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.

Key words

Cytoscape Network visualization Druggable targets Chemical biological networks Chemical networks 

Notes

Acknowledgments

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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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Iain M. Wallace
    • 1
    • 2
    • 3
  • Gary D. Bader
    • 4
    • 1
  • Guri Giaever
    • 1
    • 2
    • 3
  • Corey Nislow
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of Molecular GeneticsUniversity of TorontoTorontoCanada
  2. 2.Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
  3. 3.Department of Pharmaceutical SciencesUniversity of TorontoTorontoCanada
  4. 4.Banting and Best Department of Medical ResearchCentre for Cellular and Biomolecular Research (CCBR)TorontoCanada

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