Help:WikiPathways Webservice/AtlasMapper
From WikiPathways
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:
- 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.
- 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 |
