Integration of metabolic networks and gene expression in virtual reality

Yuting Yang^1,4, Levent Engin^1,4, Eve Syrkin Wurtele^2,4, Carolina Cruz-Neira^3,4, Julie A. Dickerson^1,4

¹Department of Electrical and Computer Engineering, ²Department of Genetics, Development, and Cell Biology and ³Department of Industrial and Manufacturing Systems Engineering, ⁴Virtual Reality Applications Center, Iowa State University, Ames, IA 50011, USA

Figure 1

Figure 1 (a) Navigating through the metabolic network in the C6 virtual environment

Figure 1 (b) Interacting with the same application in a desktop

Tweek GUI display

 

Figure 3 A user exploring a representation of gene expression levels in the C6. The plots on the left side show the clusters of genes that behave similarly. The bars through the node show the amount of variation within the cluster at each data point. The right side shows the genes that make up an individual cluster

 

Figure 4

Figure 4 A fan layout of reactions of interest focusing on GMP (the node in the center with a red label)

A fan layout of reactions of interest focusing on IMP (the node in the center with a red label) without users inside

 

Figure 6

Figure 6 Radial layouts of the ROIs focusing on AT5G35170 and AT3G60510; these genes have similar expression profiles. The magenta link indicates the DNA transcription of the RNA, the green indicates the protein translation by the RNA, the blue is the action of the resulting enzyme.  This radial layout is exploratory and represents a set of reactions with diverse reactants (yellow lines)

Same as Figure 6, without users inside

 

Metnet3DMovie.mov shows how 'AT2G22190' the putative gene for trehalose-6-phosphate phosphatase fits into the known pathways in MetNetDB. The animated portion pulled out of the main graph consists of all the reactions that gene AT2G22190 takes part in from the pathways: trehalose biosynthesis and trehalose degradation.

 

A Detailed Description of the XML file format

 

Download MetNetVR (MetNet3D) for Linux:

Instruction.pdf

MetNetVR

Runtime libraries OpenSG, R