title: Integration of metabolic networks and gene expression in virtual reality.
abstract: 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.
authors: Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
authors: Yuting
authors: Y
authors: Yang
authors: Levent
authors: L
authors: Engin
authors: Eve Syrkin
authors: ES
authors: Wurtele
authors: Carolina
authors: C
authors: Cruz-Neira
authors: Julie A
authors: JA
authors: Dickerson
mesh_terms: 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