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Integration of metabolic networks and gene expression in virtual reality.
- Source :
-
Bioinformatics (Oxford, England) [Bioinformatics] 2005 Sep 15; Vol. 21 (18), pp. 3645-50. Date of Electronic Publication: 2005 Jul 14. - Publication Year :
- 2005
-
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 to manage the data complexity.<br />Results: MetNet3D, a 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.<br />Availability: MetNet3D and some sample datasets are available at http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm.<br />Supplementary Information: Color snapshots and movies are available at http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm.
- Subjects :
- Algorithms
Arabidopsis genetics
Computer Graphics
Computer Simulation
Gene Expression
Gene Expression Regulation
Genes, Plant
Genome, Plant
Internet
Models, Biological
Multigene Family
Proteomics
Software
Software Design
Transcription, Genetic
User-Computer Interface
Biochemistry methods
Metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1367-4803
- Volume :
- 21
- Issue :
- 18
- Database :
- MEDLINE
- Journal :
- Bioinformatics (Oxford, England)
- Publication Type :
- Academic Journal
- Accession number :
- 16020466
- Full Text :
- https://doi.org/10.1093/bioinformatics/bti581