Help:Tutorial:Step 3 old
From WikiPathways
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A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a DataNode. A DataNode can have different types, in this case, we choose the type ''gene-product''. To add a gene-product click the {{TutorialImage|newgeneproduct.gif}} ''gene-product'' button, followed by clicking on the drawing area on the location that you want the element to be added. Repeat this to add 6 gene-products. You pathway now looks something like this: | A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a DataNode. A DataNode can have different types, in this case, we choose the type ''gene-product''. To add a gene-product click the {{TutorialImage|newgeneproduct.gif}} ''gene-product'' button, followed by clicking on the drawing area on the location that you want the element to be added. Repeat this to add 6 gene-products. You pathway now looks something like this: | ||
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To annotate a DataNode, go to the annotations tab in the properties dialog, by double-clicking the DataNode or choosing 'properties' from the right-click menu. Below is a screenshot of the annotation dialog: | To annotate a DataNode, go to the annotations tab in the properties dialog, by double-clicking the DataNode or choosing 'properties' from the right-click menu. Below is a screenshot of the annotation dialog: | ||
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In this dialog, you need to set the identifier, datasource and a text label that will be displayed on the pathway. You can manually fill in these values or search in the synonym database. To search for an annotation, fill in the search term and press the search button. If there are results you can select the identifier/datasource that you want to use that will automatically be filled in the ''manual entry'' fields. The text you type in the ''text label'' field will be displayed on the pathway and doesn't affect the annotation. | In this dialog, you need to set the identifier, datasource and a text label that will be displayed on the pathway. You can manually fill in these values or search in the synonym database. To search for an annotation, fill in the search term and press the search button. If there are results you can select the identifier/datasource that you want to use that will automatically be filled in the ''manual entry'' fields. The text you type in the ''text label'' field will be displayed on the pathway and doesn't affect the annotation. | ||
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After annotating a DataNode, you can click on the DataNode to see whether it's correctly annotated. If the identifier can be found in the database, the annotation info will show up in the ''Backpage'' tab of the side panel: | After annotating a DataNode, you can click on the DataNode to see whether it's correctly annotated. If the identifier can be found in the database, the annotation info will show up in the ''Backpage'' tab of the side panel: | ||
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Revision as of 17:05, 13 May 2010
The proteins of the circadian clock pathway
| Adding a gene-product |
This pathway is formed by interactions between the following proteins:
| Name | Identifier | Database |
|---|---|---|
| Bmal1 | ENSMUSG00000055116 | Ensembl |
| Clock | ENSMUSG00000029238 | Ensembl |
| Cry1 | 12952 | Entrez Gene |
| Cry2 | 12953 | Entrez Gene |
| Per1 | ENSMUSG00000020893 | Ensembl |
| Per2 | ENSMUSG00000055866 | Ensembl |
A good way to start drawing the pathway is to add the proteins. On a WikiPathways pathway, all biological entities with an annotation are stored as a DataNode. A DataNode can have different types, in this case, we choose the type gene-product. To add a gene-product click the 
gene-product button, followed by clicking on the drawing area on the location that you want the element to be added. Repeat this to add 6 gene-products. You pathway now looks something like this:
|
Annotating DataNodes
| Annotate a datanode |
Now you are going to annotate the DataNodes and set a proper text label. DataNodes can be annotated using an identifier from one of the available datasources. A pathway with annotated DataNodes has several advantages:
- Detailed information about the entity is directly available in the backpage panel
- The pathway page provides direct links to extended info at the annotation datasource website (e.g. Ensembl)
- The pathway can be used for computational analysis, e.g. visualization with GenMAPP, or statistics with Eu.gene or MAPPFinder
To annotate a DataNode, go to the annotations tab in the properties dialog, by double-clicking the DataNode or choosing 'properties' from the right-click menu. Below is a screenshot of the annotation dialog:
|
In this dialog, you need to set the identifier, datasource and a text label that will be displayed on the pathway. You can manually fill in these values or search in the synonym database. To search for an annotation, fill in the search term and press the search button. If there are results you can select the identifier/datasource that you want to use that will automatically be filled in the manual entry fields. The text you type in the text label field will be displayed on the pathway and doesn't affect the annotation.
After annotating a DataNode, you can click on the DataNode to see whether it's correctly annotated. If the identifier can be found in the database, the annotation info will show up in the Backpage tab of the side panel:
|
Note: If you try to search for Bmal1, you'll notice that it is not found. This is because this particular gene has two synonymous names (Bmal1 and Arntl1), but only the latter is stored in the internal database. However, since we have a valid Ensembl ID we can still annotate this gene manually. Just fill out the Ensembl ID and Bmal1 in the right fields. You can check the backpage to confirm that the manual entry is cross-referenced.
