latest news

1.Feb.2012

Added circular bacterial genome map

21.Sep.2010

Added new pathway map "Biosynthesis of secondary metabolites"

11.Nov.2009

Pathway Projector paper published.

19.Sep.2009

Documentation is added.

19.Jul.2009

Reference map and webpage renewal

27.Nov.2008

Beta

• Pathway Projector overview

• Zoomable User Interface

» Google Maps API

» Ext JS 2.0

• Pathway map

» KEGG Atlas

» Re-creation

• Search

• Meta word search

• Molecular mass search

» Results

• Route search

» Results

• Sequence-based search (BLAST)

» Results

• Pathway prediction (GEM System)

• Output

• Annotation

• Data mapping

• Mapping format

» Organism

» Genes

» Proteins

» Metabolites

» Time series data

» Pathway

» Organism comparison

• SOAP service

» Perl

» Python

» Ruby

• Manual editing

» XML data export

» XML data import

• Data

• Information window

» Click mode

» Mouse over mode

• Organism

• Databases

• Installation

Pathway Projector overview

• Zoomable User Interface (ZUI)

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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.

example graphic

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.

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Ext JS 2.0 is cross-browser JavaScript library to construct AJAX (Asynchronous JavaScript + XML) application.

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• Metabolic pathway

example graphic example graphic

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.

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» 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.

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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.
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