Help:DataVisualizationInCytoscape
From WikiPathways
(Difference between revisions)
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'''UNDER CONSTRUCTION''' | '''UNDER CONSTRUCTION''' | ||
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| + | 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. | ||
= Installation = | = Installation = | ||
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* Launch Cytoscape | * Launch Cytoscape | ||
| - | === WikiPathways Apps === | + | === WikiPathways and BiNGO Apps === |
* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''. | * 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'''. | * 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. When the installation is complete, click '''Close''' to exit the '''App Manager'''. | + | * 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. | 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. | ||
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[http://apps.cytoscape.org/apps/bridgedb BridgeDb app] | [http://apps.cytoscape.org/apps/bridgedb BridgeDb app] | ||
| - | === Download | + | [http://apps.cytoscape.org/apps/cluego ClueGO app] |
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| + | = Data import and mapping = | ||
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| + | === 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. | 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: [http://opentutorials.cgl.ucsf.edu/index.php/File:MusMusculus_ES-EB_25000.txt]. | The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/index.php/File:MusMusculus_ES-EB_25000.txt]. | ||
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=== Data import === | === Data import === | ||
Revision as of 18:57, 6 January 2016
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 |
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.
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: [1].
