• Pathway Projector overview
• Search
• Annotation
• Data
• Installation
Pathway Projector overview
• Zoomable User Interface (ZUI)
User Interface is developed using the popular Google Maps API, and AJAX software interface is created with Ext JS 2.0 framework. Therefore, the software interface supports interactive queries and smooth zooming with mouse scroll wheels. Users can easily annotate and edit the maps by placing custom markers, drawing lines, and by adding custom comments and annotations that can be shared among researchers.
Google Maps API enable to use in your own web pages with JavaScript, and is provided by Google. This API gets possible to control a huge image without page transition. If you want to use own large image in Google Maps API, you should divide it into several images. We used a generateGMap (G-language GAE documetation page) function of G-language GAE (Arakawa, et al., 2003)for division work.
Ext JS 2.0 is cross-browser JavaScript library to construct AJAX (Asynchronous JavaScript + XML) application.
• Metabolic pathway
The main pathway map of Pathway Projector was reconstructed from the popular KEGG Atlas (Okuda, et al., 2008) layout by adding nodes for enzymes and genes. As an example, the map for E. coli K12 contains 1365 genes, 1813 enzymes, and 1572 metabolites. Circular and rectangular nodes represent metabolites and genes/enzymes, respectively, and the names of genes, enzymes, and metabolites are displayed within the map at high zoom levels by means of semantic zooming.
» Re-creation
To calculate the midpoint of edges, all quadratic bézier curves used for the representation of reaction edges were converted into polylines for computational efficiency. Following the automatic positioning of enzyme nodes, several nodes were manually curated using Adobe Illustrator CS3 13.0.2 for layout optimization. Enzyme nodes were partitioned into multiple compartments when several genes comprised the heteromeric enzyme, with a horizontal layout for genes ≤ 6 or with two rows of up to six columns for genes ≤ 12. A list of gene names only are shown for genes > 12. As a result, the reference pathway map contains 1572 metabolite nodes and 1813 enzyme nodes. As examples of the organism specific pathways, there are 1365 gene nodes in E. coli and 2883 in human.
References
*1 Arakawa, K., et al., "G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining." Bioinformatics 2003, 19: 305-306.
*2 Okuda, S., et al., "KEGG Atlas mapping for global analysis of metabolic pathways." Nucleic Acids Res. 2008, 36: W423-426.