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Bioinformatics Advance Access published online on July 14, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti581
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received June 22, 2004
Revised April 29, 2005
Accepted July 11, 2005

Article

Integration of metabolic networks and gene expression in virtual reality

Yuting Yang 1, Levent Engin 1, Eve Syrkin Wurtele 2, Carolina Cruz-Neira 3, and Julie A. Dickerson 1*

1 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA; Virtual Reality Applications Center, Iowa State University, Ames, IA 50011, USA
2 Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA; Virtual Reality Applications Center, Iowa State University, Ames, IA 50011, USA
3 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA; Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA 50011, USA; Virtual Reality Applications Center, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed.
Julie A. Dickerson, E-mail: julied{at}iastate.edu


  Abstract

Motivation: Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and visualize due to the amount and diverse types of information that need to be represented. For example, pathway information gives indications of interactions. Experimental data such as transcriptomics, proteomics, and metabolomics data, give snapshots of the system state. Stereoscopic virtual environments provide a true three-dimensional representation of metabolic networks which can be intuitively manipulated and may help manage the data complexity.

Results: MetNet3D, a three-dimensional (3D) virtual reality system, allows a user to explore gene expression and metabolic pathway data simultaneously. Normalized gene expression data are processed in R and visualized as a 3D plot. Users can find a particular gene of interest or a cluster of genes that behave similarly and see how these genes function in metabolic networks from MetNetDB, a database of Arabidopsis metabolic networks, using animated network graphs. Interactive virtual reality, with its enhanced ability to display more information, makes such integration more effective by abstracting key relationships.

Availability: MetNet3D and some sample data sets are available at (http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm).

Supplementary Information: Color snapshots and movies are available at (http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm).


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