From WikiPathways

UNDER CONSTRUCTION

This tutorial describes how to visualize experimental data on WikiPathways in Cytoscape. After importing the data, it is mapped to Ensembl identifiers using BridgeDb. A visual style is created, and the data is visualized on pathways imported from WikiPathways. Finally, over-representation analysis is done with the ClueGO app.

Contents 1 Installation 1.1 Cytoscape 1.2 WikiPathways and BiNGO Apps 2 Data import and mapping 2.1 Download the data 2.2 Data import 2.3 Identifier mapping with BridgeDb 3 Viewing data on pathways 3.1 Open WikiPathways in Cytoscape 3.2 Visual Styles

Installation

Cytoscape

• Download Cytoscape here: http://www.cytoscape.org/.
• Launch Cytoscape

WikiPathways and BiNGO Apps

• In Cytoscape, open the App Manager under Apps > App Manager.
• In the search field, type WikiPathways to search for the WikiPathways app. In the search results, select the WikiPathways app and click Install.
• Next, find and install the BridgeDb app in the same way.
• Repeat the process for the ClueGO app. When the installation is complete, click Close to exit the App Manager.

Alternatively, Cytoscape apps can be installed directly from the Cytoscape App Store. If Cytoscape is open on your computer, you can click Install on the relevant app page, and the app will install.

WikiPathways app

BridgeDb app

ClueGO app

Data import and mapping

Download the data

For this tutorial, we will use an example dataset of transcriptional profiling of mouse embryonic stem cells and embryoid bodies. The data is in the form of a text file.

The experimental data for this tutorial can be found here: MusMusculus_ES_EB.txt.

Data import

Identifier mapping with BridgeDb

Viewing data on pathways

Open WikiPathways in Cytoscape

Visual Styles