Help:Tutorial:Step 6
From WikiPathways
Target genes are activated by the E-box element
| Drawing the transcription of mPer/mCry and degradation of mPer |
After the Clock/Bmal1 dimer binds to the E-box element, transcription of several target genes are activated. This simplified version of the Circadian clock pathway, will restrict to the mPer/mCry genes, which will act as a negative feedback loop. As long as Per1 or Per2 exist as monomers, they will be phosphorylated by casein kinase 1 delta or epsilon, followed by degradation. In the pathway drawing we simplify it a bit by leaving out the phosphorylation event, resulting in the following representation:
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1. Stack the mCry/mPer DataNodes
To illustrate that the mCry/mPer genes are activated by the E-box element, we can stack them below the 'Gene' label. Place the mPer/mCry DataNodes below the 'Gene' label and stack them vertically, using the 
stack vertically button.
2. Copy the gene-products
The genes will be translated into proteins, to show this on the pathway, copy the stacked genes and move them to the right of the stacked DataNodes. Separate the mPer DataNodes from the mCry DataNodes to show that they exist as seperate proteins.
3. Draw a line from the genes to the gene-products
To illustrate that the genes are translated into proteins, we draw a dashed arrow from the stacked genes to the copied genes.
5. Create a degradation shape
As long as Per1 or Per2 is not dimerized with Cry1 or Cry2, it will be degraded. We can indicate degradation by using the degradation shape:
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You will notice that this shape is not on the toolbar, so to insert it, we have to insert another shape (e.g. a rectangle) and change it's Shape Type property. Insert a rectangle, select it and change the Shape Type property in the properties table to mim-degradation:
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When you selected mim-degradation as property, you will see the rectangle change into a degradation shape.
5. Draw an arrow from the mPer DataNodes to the degradation shape
To show that the mPer proteins are degraded, draw an dashed arrow from the two mPer DataNodes to the degradation shape.
6. Create groups and connect the lines
| Grouping the elements |
Finally, you have to properly group the elements and link the lines that were added. Here we will use nested groups (groups within other groups), so the order of grouping and linking is important. We can create the following groups:
- the Per1/2 and Cry1/2 genes under the Gene label
- group of Per and Cry pairs
- the Per1/2 gene-products
- the Cry1/2 gene-products
The video on the right shows the order of linking and grouping. Start with creating the lowest level groups (group 1, 2.1 and 2.2). Link the 'degradation line' to the degradation shape and group 2.1. Now select group 2.1 and 2.2 and group the selection to create group 2 (by selecting Group->Group in the right-click menu or pressing CTRL-G). Link the line that represents the translation of mPer and mCry to groups 1 and 2. You can test whether you correctly linked the line by moving the groups and see if the correct line moves along.
