Help:Tutorial:Step 2 v2

From WikiPathways

Revision as of 23:14, 16 November 2015

This step includes several aspects of pathway creation, from creating a pathway at WikiPathways, launching the Applet Editor, adding data nodes, interactions and annotations. Written instructions correspond to the embedded video.

Create a new pathway

Open a new browser window or tab, go to the WikiPathways main page and click the image under the header Create in the Contributing New Pathways section. You can also click the Create link in the left-hand side panel. Enter Demo_yourname under the Pathway name field and select Homo sapiens in the species menu. Now click the Create pathway button.

After clicking the button, a new page will open and the pathway editor will be loaded.

Open the editor in a separate window by clicking the Switch to fullscreen mode button. This allows you to resize the editor and edit fullscreen. You can return to the original editor in your browser by clicking the Switch to embedded mode button.

Adding initial gene products and metabolites

For the purposes of this tutorial, we will use the Statin pathway as our example. On a WikiPathways pathway, all biological entities with an annotation are stored as a DataNode.

• To start, click the drop-down next to the GENE button and select Metabolite. Place the metabolite on the drawing board by dragging and dropping it.

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 the node, double-click the metabolite to bring up the DataNode properties interface. Type in 3-hydroxy-3-methylglutaryl-coA and click Search. (Note that you can also manually fill in identifier and data source.)
• In the search results, select the node with the HMDB identifier HMDB01375. Click OK.
• Back in the DataNode properties window, you can alter the text label that will used for the metabolite. In this case, change it to HMG-CoA. Click OK to save.
• Repeat the steps above and add another metabolite node for Mevalonate. Place it under the HMG-CoA node.

Add interactions

Next, we need to connect the two metabolites:

• In the drop-down next to the Interaction button, select Conversion from the MIM interactions section. Place the interaction on the drawing board.
• To attach the interaction, click on the non-arrow end of the interaction to select it, and drag it towards the HMG-CoA node. Red snap targets on the node will become visible as you drag the interaction towards it. Hover over a snap target to select it; it will be highlighted in green when selected. Simply let go of the interaction when you see the target highlight, and the interaction will attach.
• Repeat the process to attach the arrow-end of the interaction to Mevalonate.
• Once the two nodes are connected, you can move them by clicking and dragging to adjust the alignment and layout.

Add enzymatic reaction

We can now add the enzyme that converts HMG-CoA to Mevalonate, HMGCR:

• Add another data node of the GeneProduct and annotate it as HMGCR.
• Add an interaction of type Catalysis (under MIM interactions).
• Connect the start (plain) end of the catalysis to the left short-end of HMGCR.

The catalysis interaction works on the existing interaction between HMG-CoA and Mevalonate. To connect the catalysis interaction to this interaction, we first need to add an anchor to the conversion interaction.

• To add an anchor, right-click on the conversion interaction and select Add anchor. You can adjust the position of the anchor by click and drag.
• Attach the catalysis interaction to the anchor.

Add inhibition of the catalysis by Statin

We can now add the inhibition of the catalysis by Statin.

• Add another metabolite data node. In the DataNode properties interface, search for Statin. There will be multiple results, choose Pravastatin. For simplicity, change the text label to Statin.
• Now, add an interaction of type Inhibition (under MIM interactions) and connect the plain end to the Statin node.
• Add an anchor on the HMGCR catalysis interaction.
• Connect the inhibition end of the new interaction to the anchor.
• To make the interactions easier to read, change the style of the inhibition interaction to an elbow. You can do this by right-clicking the interaction and selecting Line type > elbow.

Changing the color and style of interactions

Inhibitions are often depicted as red in pathway illustrations, so in keeping with this convention, let's change the color of the inhibition to red:

• Select the inhibition interaction.
• In the right-side Properties panel, change the color to red.

Saving changes and adding a description

• To save the pathway, click the Save the pathway to WikiPathways.org button.
• Exit full-screen mode by clicking the Switch to embedded mode button.