Help:WikiPathways Webservice/AtlasMapper

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(New page: The WikiPathways / Atlas mapper is an example of a web application that integrates external data with pathways from WikiPathways. This tool visualizes differentially expressed genes from t...)
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The WikiPathways / Atlas mapper is an example of a web application that integrates external data with pathways from WikiPathways. This tool visualizes differentially expressed genes from the [http://www.ebi.ac.uk/microarray-as/atlas/ ArrayExpress Atlas] repository on pathways from WikiPathways.
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__NOTOC__
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* [http://137.120.14.13:8180/atlas-mapper/AtlasMapper.html Try it out yourself]
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<div class="frontPagePanel redBg" style="width:100%"><div class="redFg" style="width:100%;text-align:center"><big><b>This web service showcase has been discontinued!</b></big></div><p>The ArrayExpress Atlas team discontinued the SOAP service that was used by this showcase, so we are no longer able to support it. This page will be kept online for reference, you can still look at the source code for examples of how to use the WikiPathways web service.</p></div>
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* Or [http://137.120.14.13:8180/atlas-mapper/AtlasMapper.html#pathway=WP251&factortype=light&factorvalues=12%20h%20light:12%20h%20dark;Constant%20darkness&panel=image view an example visualization]
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= WikiPathways and ArrayExpress Atlas =
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The WikiPathways / Atlas mapper is an example of a web application that integrates external data with pathways from WikiPathways. This tool visualizes differentially expressed genes from the [http://www.ebi.ac.uk/microarray-as/atlas/ ArrayExpress Atlas] repository on pathways from WikiPathways.
== Manual ==
== Manual ==
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* White: No data was found ArrayExpress Atlas for the selected condition
* White: No data was found ArrayExpress Atlas for the selected condition
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If you selected more than one condition, the genes will be divided in multiple boxes. You can click on a gene to see the p-values for each condition and view the gene details on [http://www.ensembl.org Ensembl] or explore the expression profiles on [ArrayExpress Warehouse http://www.ebi.ac.uk/microarray-as/aew/]
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For more information on how the p-values are calculated, see the [http://www.ebi.ac.uk/microarray/doc/atlas/details.html explanation on the Atlas website].
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If you selected more than one condition, the genes will be divided in multiple boxes. You can click on a gene to see the p-values for each condition and view the gene details on [http://www.ensembl.org Ensembl] or explore the expression profiles on [http://www.ebi.ac.uk/microarray-as/aew/ ArrayExpress Warehouse]
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== Source code ==
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This application was built with the Google Web Toolkit, the wikipathways-client and PathVisio libraries. You can find the source code here:
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http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/AtlasMapper
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== Statistics ==
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The table below shows statistics on the coverage of Atlas data on WikiPathways pathways as of 10 June 2009.
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{| class="prettytable sortable"
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! Organism
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! Genes on WikiPathways
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! Genes containing Atlas data
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! Conditions
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! Experiments
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|- align="center"
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|Caenorhabditis elegans
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|474
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|163
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|22
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|4
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|- align="center"
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|Danio rerio
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|778
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|336
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|68
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|8
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|- align="center"
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|Drosophila melanogaster
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|522
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|339
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|98
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|24
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|- align="center"
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|Homo sapiens
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|3398
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|3068
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|1646
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|288
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|- align="center"
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|Mus musculus
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|3399
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|3000
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|889
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|253
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|- align="center"
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|Rattus norvegicus
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|2360
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|1770
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|416
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|102
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|- align="center"
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|Saccharomyces cerevisiae
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|851
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|681
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|130
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|37
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|}
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----
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[[Help:WikiPathways_Webservice|Return to Web Services help page]]

Current revision


This web service showcase has been discontinued!

The ArrayExpress Atlas team discontinued the SOAP service that was used by this showcase, so we are no longer able to support it. This page will be kept online for reference, you can still look at the source code for examples of how to use the WikiPathways web service.

WikiPathways and ArrayExpress Atlas

The WikiPathways / Atlas mapper is an example of a web application that integrates external data with pathways from WikiPathways. This tool visualizes differentially expressed genes from the ArrayExpress Atlas repository on pathways from WikiPathways.

Manual

To visualize data on a pathway, you need to perform the following steps:

  1. Select a pathway: Just start typing the name or identifer of the pathway you want to visualize and select it from the list that appears.
  2. Select experimental conditions: First select the condition type (e.g. organism part, strain or disease) and then check the boxes for the conditions you want to visualize on the pathway.

After completing these two steps, you will see an image of the pathway where genes are colored according to the following scheme:

  • Red: The gene was found up-regulated for this condition
  • Blue: The gene was found down-regulated for this condition
  • Gray: The gene was found both up and down regulated in different experiments
  • White: No data was found ArrayExpress Atlas for the selected condition

For more information on how the p-values are calculated, see the explanation on the Atlas website.

If you selected more than one condition, the genes will be divided in multiple boxes. You can click on a gene to see the p-values for each condition and view the gene details on Ensembl or explore the expression profiles on ArrayExpress Warehouse

Source code

This application was built with the Google Web Toolkit, the wikipathways-client and PathVisio libraries. You can find the source code here:

http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/AtlasMapper

Statistics

The table below shows statistics on the coverage of Atlas data on WikiPathways pathways as of 10 June 2009.

Organism Genes on WikiPathways Genes containing Atlas data Conditions Experiments
Caenorhabditis elegans 474 163 22 4
Danio rerio 778 336 68 8
Drosophila melanogaster 522 339 98 24
Homo sapiens 3398 3068 1646 288
Mus musculus 3399 3000 889 253
Rattus norvegicus 2360 1770 416 102
Saccharomyces cerevisiae 851 681 130 37

Return to Web Services help page

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