As input GeneNetFinder takes either gene expression data or regulation rules.
Load gene expression data: load the raw value of gene expression data in text file.
Load regulation rules: load regulation rules of gene regulatory networks in .rule format.
Exit: Quit the program.
Menu - Operations:
After loading the gene expression data, click "Visualize identified gene regulations" to visualize a
gene regulatory network. GeneNet Finder provides two layout methods:
Grid Layout: gene regulatory network as an orthogonal drawing with nodes in grid points.
Layered layout: gene regulatory network as a layered graph.
Circle layout: visualizing gene regulatory networks in circle.
Click "Save image as" to save your visualization.
Menu - Data:
Click "Analyze input data" to analyze the gene expression data.
The menu "Identified gene regulations" shows the identified gene regulations from the input data.
Save identified regulations as: save your result.
Menu - Options:
View regulations identified: show or hide the regulations identified panel.
View Node list: show or hide the node list listbox.
Setting: more settings of GeneNet Finder.
Menu - Setting:
Some settings of GeneNet Finder
Show identified regulations: set/unset the default setting of the regulations identified panel.
Show node list: set/unset the default setting of the node list listbox.
Show edge labels: set/unset the default setting of edge labels.
Interface:
Analysis of gene expression data
Setting time points
Identified gene regulations
Recommended operational process:
File -> Load gene expression data -> Operations -> Visualize identified regulations -> Save (image/regulations)
File -> Load regulation rules -> Layout -> Grid layout/ Circle layout -> File -> Save as image
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Biocomputing Lab, School of Computer Science and Engineering, Inha University.
Incheon, 402-751, South Korea. Phone: +82-32-8607388, Fax: +82-32-8634386