Help:DataVisualizationInCytoscape
From WikiPathways
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| - | This tutorial | + | '''This tutorial has been replaced by the [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title WikiPathways App Tutorial].''' |
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= Installation = | = Installation = | ||
=== Cytoscape === | === Cytoscape === | ||
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* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''. | * In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''. | ||
| - | [[image:AppManager.png|left|]]<br clear="all" /> | + | [[image:AppManager.png|650px|left|]]<br clear="all" /> |
* In the search field, type ''WikiPathways'' to search for the WikiPathways app. Select the WikiPathways app from the results and click '''Install'''. | * In the search field, type ''WikiPathways'' to search for the WikiPathways app. Select the WikiPathways app from the results and click '''Install'''. | ||
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* In the pathway results, select the Electron Transport Chain and either double-click on the entry to open, or click on the '''Import as Pathway''' button at the bottom right. Once opened, the pathway should look like this: | * In the pathway results, select the Electron Transport Chain and either double-click on the entry to open, or click on the '''Import as Pathway''' button at the bottom right. Once opened, the pathway should look like this: | ||
| - | [[image:WPSearchResults.png|left|]]<br clear="all" /> | + | [[image:WPSearchResults.png|900px|left|]]<br clear="all" /> |
Once the pathway opens in Cytoscape, it should look like this: | Once the pathway opens in Cytoscape, it should look like this: | ||
| - | [[image:ElectronTransport.png|left|]]<br clear="all" /> | + | |
| + | [[image:ElectronTransport.png|1100px|left|]]<br clear="all" /> | ||
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* Repeat the steps above to search for ''Proteasome'' and import the '''Proteasome degradation''' pathway. | * Repeat the steps above to search for ''Proteasome'' and import the '''Proteasome degradation''' pathway. | ||
* You should now have both pathways open in Cytoscape: | * You should now have both pathways open in Cytoscape: | ||
| - | [[image:PathwaysInCytoscape.png|left|]]<br clear="all" /> | + | [[image:PathwaysInCytoscape.png|1100px|left|]]<br clear="all" /> |
=== Identifier Mapping === | === Identifier Mapping === | ||
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** To: '''Entrez''' | ** To: '''Entrez''' | ||
* Then click '''OK''' | * Then click '''OK''' | ||
| - | * Now you have a new column of Entrez Gene IDs (all the way to the right) | + | * Now you have a new column of Entrez Gene IDs (all the way to the right) |
| + | '''Note that the WikiPathways app automatically adds Ensembl identifiers to pathways upon import. This means that manually annotating the pathway is only necessary if the data is annotated with a system other than Ensembl.''' | ||
= Data import = | = Data import = | ||
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=== Import data to Cytoscape === | === Import data to Cytoscape === | ||
| - | * To import the experimental data, select '''File > Import > Table | + | * To import the experimental data, select '''File > Import > Table from File...'''. Select the ''starvation_dataset_trans.txt'' file and click '''Open'''. |
* Under '''Where to Import Table Data''', choose '''To selected networks only'''. | * Under '''Where to Import Table Data''', choose '''To selected networks only'''. | ||
* To select both pathways, click the '''Select All''' button. | * To select both pathways, click the '''Select All''' button. | ||
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* For the purposes of this tutorial, click the key symbol. This defines the '''ensid''' column as being the key column, which will be used to link the data to the pathways. | * For the purposes of this tutorial, click the key symbol. This defines the '''ensid''' column as being the key column, which will be used to link the data to the pathways. | ||
| - | [[image:DataImport.png|left|]]<br clear="all" /> | + | [[image:DataImport.png|600px|left|]]<br clear="all" /> |
* Click '''OK''' to import the data. | * Click '''OK''' to import the data. | ||
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[[image:ExportPathway.png|left|]]<br clear="all" /> | [[image:ExportPathway.png|left|]]<br clear="all" /> | ||
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Current revision
This tutorial has been replaced by the WikiPathways App Tutorial.
