latest news

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

Search

example graphic example graphic

The search box in the top right corner becomes the entrance of every search. Users can search metabolites, enzymes, genes, mass of compounds and KEGG ID (Compound, enzyme, orthology ID) from the box. The results will be displayed on subwindow in the right side.

• Meta word search

Users can search every components in the metabolic pathway with any words.
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• Molecular weight search

When users search from molecular weight, just input a number.
  • 10-20
The case of looking for metabolites within 20 from 10.
  • 10
When users input a number, the result shows metabolites within ±10 of inputted number. In this case, the subwindow will show slider bar to change the range.
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Search results
route

The all results are listed at right panel with names. Since these lists link to the target component, when users click the name, the target component open own information window. Likewise, a red pin stands on the node of search results, and information window is opened when users click it.

route
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• Route search

example graphic

When users search path search, set 2 points as start and end. Each metabolite is specified from information window. Users click a in each information window of any metabolite that users want to set start or end metabolite. This function is supported by KEGG.

1st step : After open the information window of the start node, click the "start point" button.
route

2nd step : A yerrow pin will appear on the start node.
route
3rd step : Nextly, you should select end point and click the "end point" button in the information window.
route
Search results

Wait a few minutes until return to pathway map. All route candidates are listed at the right panel with each colors. You can select a route and the route is drew on the edges with the same color.

route
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• Sequence-based search (BLAST)

example graphic

A sequence similarity search using nucleotide or amino acid sequences has been implemented based upon KEGG BLAST. The system automatically interprets the type of sequence (nucleotide or protein) and subsequently chooses the appropriate program (blastn, blastp, blastx, tblastx); therefore, the user only needs to paste in a sequence of interest to the text area and choose the type of database to run the BLAST search. The search results are marked with highlighted edges on the reference pathway and are also listed in the search result panel with KEGG Orthology identifiers, species names, e-values, and links to organism-specific pathway maps with the BLAST result. The "Pathway Prediction" tab, which is another tool that can be found in the "Tools" window, reconstructs the pathway from given multi-FASTA amino acid files and draws the resulting pathway map accompanied by corresponding e-values. Users can use this feature to analyze novel organisms that are not included in Pathway Projector or to analyze pathways in any given gene set, such as those included in an environmental metagenome database.

In the KEGG BLAST tab window on the tools, Input sequence data and select database type (nucleotide or protein). Therefore, this system decides the BLAST program automatically based upon inputted data and selected database type. After the program selected, please click the submit button.

route
Search results
route

Wait a few minutes until return to pathway map. The BLAST results are shown at the right panel with e-value, organism name and KEGG ortholog ID. When users click some organism map button, Pathway Projector create a new tab with organism specific pathway map and BLAST result. Similar to other search, these lists are linking to node information window.

route
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• Pathway prediction (GEM System)

The Pathway prediction tool reconstructs the pathway from given multi-FASTA sequence files using BLAT and SwissProt using the GEM System (Arakawa, et al., 2006).



route

• Outputs

All of the search results are downloadable from this "Download search results" button.


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References

*1 Arakawa, K., et al., "GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes." Bioinformatics 2006, 7: 168.
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