Help:Tutorial:Step 3 old

From WikiPathways

---

Revision as of 14:06, 18 February 2008

Next step | Index

The proteins of the circadian clock pathway

This pathway is formed by interactions between the following proteins:

Name	Identifier	Database
Bmal1 (or Arntl)	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

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:

Next step | Index