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Bioinformatics Advance Access published online on July 25, 2008
Bioinformatics, 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,*

1 State 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
2 Department of Biochemistry, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada H3A 1A4

*To whom correspondence should be addressed. Jingkang Shen, E-mail: jkshen{at}mail.shcnc.ac.cn


  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 isomor-phism, 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 avail-able for download at http://202.127.30.184:8080/software.html

Contact: JingKang Shen Email: jkshen{at}mail.shcnc.ac.cn

Associate Editor: Prof. Alfonso Valencia

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

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