Help:Tutorial

From WikiPathways

This tutorial explains how to create a pathway on WikiPathways, using the circadian clock pathway as an example.

The circadian clock pathway

The circadian clock is a molecular mechanism that maintains the cell's 24-hour molecular rhythm by driving the rhythmic expression of a wide range of genes, involved in metabolism, physiology and behaviour. In this tutorial, you will draw a simplified version of the pathway, restricting to the mPer/mCry feedback loop.

Step by step guide to drawing the circadian clock pathway

The following pages show you step-by-step how to draw a simplified version of the circadian clock pathway as described in the section above.

• Step 1: Log in to WikiPathways
• Step 2: Create a new pathway
• Step 3: The proteins of the circadian clock pathway
• Step 4: Illustrate the E-box enhancer
• Step 5: Clock and Bmal1 dimerize and bind to the E-box element
• Step 6: Target genes are activated by the E-box element
• Step 7: The negative feedback loop
• Step 8: Draw cellular locations
• Step 9: Adding bibliography
• Step 10: Adding a description
• Step 11: Adding a curation tag

Advanced tutorials

Use the circadian clock pathway in GenMAPP

The next tutorial shows you how use the pathway you created to visualize experimental data with GenMAPP.

• GenMAPP tutorial

Extend and layout pathways using Cytoscape

Cytoscape is a tool for network visualization and analysis. In the following tutorials we will highlight some of the Cytoscape functionality that is relevant for the pathways as used on WikiPathways. For tutorials of other Cytoscape features, please see the Cytoscape wiki. The following tutorials will show two plugins at work, the Agilent Literature Search plugin and the Bubblerouter plugin.

• Cytocape and Agilent Literature Search
• Cytoscape and the Bubblerouter plugin

Analyzing data with PathVisio

These tutorials show you how to use WikiPathways pathways in PathVisio.

• Tutorial on analyzing microarray data
• Tutorial on analyzing metabolomics data

Commonly used terms

Sidepanel

The panel containing the Properties and Backpage tabs (see screenshot 1B).

Drawing area

The area on which the pathway is drawn (see screenshot 1A).

Property table

The table where you can edit properties of the currently selected object(s). The property

table is located in the sidepanel under the tab named 'Properties'.

Backpage browser

A panel that gives detailed annotation info on the currently selected DataNode. The Backpage browser

is located in the sidepanel under the tab named 'Backpage'.

Toolbar

see screenshot 1C.

Infobox

Displays information about the pathway (see screenshot 1D).

Screenshot 1: the editor applet