Integration of metabolic networks and gene expression in virtual reality
Yuting Yang1,4,
Levent Engin1,4,
Eve Syrkin Wurtele2,4,
Carolina Cruz-Neira3,4,
Julie A. Dickerson1,4
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
Figures Tables Animation Layout Algorithms XML File Format
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
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 5
Figure5 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 5, without users inside
|
Node Type |
Glyph Shape and Size |
Glyph Color |
|
Metabolite node (Substrate or product) |
Sphere, Large |
Yellow |
|
Reaction node |
Sphere, Small |
Yellow |
|
Protein complex node |
Cube, Small |
Blue |
|
Polypeptide node |
Cube, Small |
Red |
|
RNA node |
Cube, Small |
Green |
|
Gene Node |
Cube, Small |
Magenta |
Table 1. Shape, size and color encoding for nodes.
|
Reaction Type |
Edge Color |
|
Enzymatic (from a substrate node to a reaction node, or from a reaction node to a product node) |
Yellow |
|
Catalysis (from a protein complex node to a reaction node, or from a polypeptide node to a reaction node) |
Blue |
|
Assembly (from a polypeptide node to a protein complex node) |
Red |
|
Translation (from RNA node to polypeptide node) |
Green |
|
Transcription (from gene node to RNA node) |
Magenta |
|
Negative regulation |
Green |
|
Positive regulation |
Yellow |
Table 2. Color encoding for edges. The reaction node is introduced to convert the multiple (substrates) to multiple (products) relationship to a set of one (substrate or product) to one (reaction node) relationship.
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
