Tutorial:WikiPathways App

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Introduction

The WikiPathways app lets you import pathways from WikiPathways into Cytoscape, as well as open locally stored GPML (GenMAPP Pathway Markup Language) files.

Install the WikiPathways App either from within Cytoscape 3 (Apps → App Manager) or directly from the Cytoscape app store.

Import a pathway from WikiPathways

  1. Go to File → Import → Network → Public Databases....
  2. Under Data Source choose WikiPathways.

WikiPathways Plugin interface

  1. In the search field at the top, enter a search term, for example p53 or apoptosis. Press Return to search all species, or to restrict the search to a particular species, check the Only check box and select the species of interest from the drop-down menu. Press Return from within the search field.
  2. In the search results, double-click on any pathway to open it. By default, pathways are imported with the original pathway layout, but you can also select to Import as a Network from the pulldown button at the bottom. The images below illustrate the difference between these two modes.
  3. You can also Open in Web Browser to view a selected pathway at WikiPathways.org.

Apoptosis pathway Apoptosis network

Note that if the pathway representation contains incomplete interactions, you will see a warning message upon import saying "Some of the lines in the pathways are not connected. Therefore some nodes might not be connected".

Open a local gpml file

  1. Go to File → Import → Network → File.... Select a local gpml file and click Open.
  2. A Set Parameters dialog will appear where you can choose to open the pathway as a Pathway or Network. Click OK to continue.