Integration of metabolic networks and gene expression in virtual reality.
BACKGROUND
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.


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.


BACKGROUND
MetNet3D and some sample datasets are available at http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm.


BACKGROUND
Color snapshots and movies are available at http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryInformation.htm.
Yang
Yuting
Y
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
Engin
Levent
L
Wurtele
Eve Syrkin
ES
Cruz-Neira
Carolina
C
Dickerson
Julie A
JA
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001671:Biochemistry / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D015870:Gene Expression; D005786:Gene Expression Regulation; D017343:Genes, Plant; D018745:Genome, Plant; D020407:Internet; D008660:Metabolism; D008954:Models, Biological; D005810:Multigene Family; D040901:Proteomics; D012984:Software; D012985:Software Design; D014158:Transcription, Genetic; D014584:User-Computer Interface