Help:Tutorial:Step 3 v2

From WikiPathways

This step explains how to add cellular compartment information, illustrating transport out of the cell, use of labels, copy and paste, creating and connecting complexes and adding a literature reference. Written instructions correspond to the embedded video.

This tutorial starts with a few more entities added to the Demo pathway. You can either add the remaining entities manually, or start with the Demo_part3 pathway. Starting with the Demo_part3 pathway, we have all the intracellular components of the pathway. The next steps include adding a cellular compartment, and illustrating the translocation of Cholesterol out of the cell. First, open the editor and start full-screen mode.

Add a cellular compartment

• To add a cellular compartment shape to the pathway, select the Cell shape from the right-side Objects panel and place it on the drawing board.
• Size and position the cell shape to fit all the pathway entities. The cell shape should be a large rectangle.

Adding labels

When using cellular compartments in a pathway, add labels for clarity:

• In the toolbar, click the Label button and place it at the bottom right corner of the cell shape.
• Double-click the label to open the Label properties interface, and type in Liver cell. In this interface you can also change the font style and size of the label.
• Repeat these steps to add another label just outside the cell shape, for Plasma.

Label text and style can also be edited in the Properties tab of the right-side panel.

Illustrating transport

To illustrate the transport of cholesterol out of the liver cell, we place a copy of the cholesterol node in the area representing plasma:

• Select the cholesterol node, and click the Copy selected pathway objects to clipboard button in the toolbar.
• Next, click the Paste pathway objects from clipboard button . This creates a new copy of the cholesterol node.
• Place the copy of the node outside the liver cell, under the original copy of the cholesterol node.

Creating and connecting complexes

The transport of cholesterol out of the liver cell is facilitated by a transfer protein complex, composed of MTTP and PDIA2.

• Add two new GeneProduct data nodes and annotate them as PDIA2 and MTTP.
• Select both nodes either by Command+Click or click and drag.
• In the toolbar, click the Stack vertical center button to stack the nodes.
• To create a complex, first select the two nodes again and then right-click and select Create complex.
• Place the complex in the plasma membrane, under SOAT1.

Next, we can illustrate the transfer of cholesterol by adding an interaction:

• Add an interaction of type MIM conversion and connect it to go from the intracellular cholesterol node to the extracellular cholesterol node.
• Next, add an anchor to the interaction.
• Add a new interaction of type MIM catalysis.
• Connect the catalysis interaction from the MTTP/PDIA2 complex to the anchor on the transfer interaction.
• Finally, move the complex to the right so that it is placed in the plasma membrane on the cholesterol transfer interaction.

Adding a literature reference

Since we have a literature reference describing how MTTP/PDIA2 facilitates cholesterol transfer, we can add it to the MTTP/PDIA2 complex:

• To add a literature reference to the complex, right-click on the complex and select Literature > Add literature reference.
• In the Literature reference properties type in the PMID for the reference and click Search. When the PMID is found, the fields are completed.
• Double-check that the correct reference was found, then click OK.
• Save your pathway to WikiPathways, and enter a description for your changes when prompted.
• Exit full-screen mode and close the editor.