| Chapter title |
Displaying chemical information on a biological network using Cytoscape.
|
|---|---|
| Chapter number | 18 |
| Book title |
Network Biology
|
| Published in |
Methods in molecular biology, July 2011
|
| DOI | 10.1007/978-1-61779-276-2_18 |
| Pubmed ID | |
| Book ISBNs |
978-1-61779-275-5, 978-1-61779-276-2
|
| Authors |
Iain M. Wallace, Gary D. Bader, Guri Giaever, Corey Nislow |
| Editors |
Gerard Cagney, Andrew Emili |
| 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. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 4 | 14% |
| Austria | 2 | 7% |
| Canada | 1 | 4% |
| Sweden | 1 | 4% |
| Unknown | 20 | 71% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 9 | 32% |
| Student > Master | 4 | 14% |
| Student > Ph. D. Student | 3 | 11% |
| Student > Doctoral Student | 2 | 7% |
| Other | 2 | 7% |
| Other | 6 | 21% |
| Unknown | 2 | 7% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 9 | 32% |
| Agricultural and Biological Sciences | 7 | 25% |
| Computer Science | 4 | 14% |
| Medicine and Dentistry | 3 | 11% |
| Chemistry | 2 | 7% |
| Other | 2 | 7% |
| Unknown | 1 | 4% |