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Bioinformatics Advance Access originally published online on July 25, 2008
Bioinformatics 2008 24(18):2117-2118; doi:10.1093/bioinformatics/btn389
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks

Bing Xiong 1, Ke Liu 1, Jie Wu 1, David L. Burk 2, Hualiang Jiang 1 and Jingkang Shen 1,*

1State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai, China 201203 and 2Department of Biochemistry, McGill University, 740 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1A4

*To whom correspondence should be addressed.


  Abstract

Summary: DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome. DrugViz can import drug–target network information in an extended SIF file format to Cytoscape and display the two-dimensional (2D) structures of small molecule nodes in a unified visualization environment. It also can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches. After selections, users can furthermore conduct a two-side clustering analysis on drugs and targets, which allows for a detailed analysis of the active compounds in the network, and elucidate relationships between these drugs and targets. DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology.

Availability: DrugViz and data set used in Application are freely available for download at http://202.127.30.184:8080/software.html

Contact: jkshen{at}mail.shcnc.ac.cn

Associate Editor: Alfonso Valencia

Received on May 22, 2008; revised on May 22, 2008; accepted on July 23, 2008

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