Help:DataVisualizationInCytoscape

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'''UNDER CONSTRUCTION'''
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'''This tutorial has been replaced by the [https://cytoscape.org/cytoscape-tutorials/protocols/wikipathways-app/#/title WikiPathways App Tutorial].'''
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<!--
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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.
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= Installation =
= Installation =
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=== Cytoscape ===
=== Cytoscape ===
* Download Cytoscape here: http://www.cytoscape.org/.
* Download Cytoscape here: http://www.cytoscape.org/.
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* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''.
* In Cytoscape, open the '''App Manager''' under '''Apps > App Manager'''.
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[[image:AppManager.png|left|]]<br clear="all" />
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[[image:AppManager.png|650px|left|]]<br clear="all" />
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* In the search field, type ''WikiPathways'' to search for the WikiPathways app. In the search results, select the WikiPathways app and click '''Install'''.
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* 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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* Next, find and install the BridgeDb app in the same way. When the installation is complete, click '''Close''' to exit the '''App Manager'''.
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* 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/wikipathways WikiPathways app]
[http://apps.cytoscape.org/apps/wikipathways WikiPathways app]
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[http://apps.cytoscape.org/apps/bridgedb BridgeDb app]
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= Pathway import and mapping =
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=== Import pathways from WikiPathways ===
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Based on over-representation analysis, two pathways have been identified as significant for this dataset. To start, we will open these pathways.
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* Locate the search field at the top of the Network Panel and choose WikiPathways from the pulldown options.
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* Type in ''Electron Transport'' and hit '''Enter''' or click the icon to search.
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* In the results dialog, check the  box for '''Only''' and select '''Mus musculus''' in the species drop-down.
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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:
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[[image:WPSearchResults.png|900px|left|]]<br clear="all" />
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Once the pathway opens in Cytoscape, it should look like this:
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[[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.
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* You should now have both pathways open in Cytoscape:
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[[image:PathwaysInCytoscape.png|1100px|left|]]<br clear="all" />
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=== Identifier Mapping ===
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In the Table Panel you can see that the gene identifiers in these pathways from Ensembl. It turns out that the experimental data we will be using in this example is also annotated with Ensembl identifiers. But this is not always the case! Fortunately, it is very easy to get a new column of identifiers in any of the major types.  In this example, we will go ahead and add a column of Entrez Gene IDs to demonstrate this functionality.
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* In the Table Panel, right click on the column header '''XrefId''' which contains the identifiers for the data nodes.
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* Choose '''map column''' to bring up the ID Mapping dialog
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* Select the following:
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** Species: '''Mouse'''
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** Map from: '''Ensembl'''
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** To: '''Entrez'''
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* Then click '''OK'''
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* Now you have a new column of Entrez Gene IDs (all the way to the right)
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= Data import and mapping =
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'''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.'''
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=== Download the data ===
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= Data import =
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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.  
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=== Download data ===
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For this tutorial, we will use an example dataset describing intestinal changes in response to fasting in mice. The data gene expression array data, and is in the form of a text file.  
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The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/images/7/75/MusMusculus_ES-EB_25000.txt MusMusculus_ES_EB.txt].
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The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/images/f/f7/Starvation_dataset_trans.txt Starvation_dataset_trans.txt].
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=== Data import ===
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Source: [http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-361 Sokolovic et al. BMC Genomics. 2007 Oct 9;8:361]
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* To import the experimental data, select '''File > Import > Table > File...'''. Select the ''MusMusculus_ES_EB.txt'' file and click '''Open'''.
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* Choose a name for the new data table, for example '''ES_EB'''. Click '''OK''' to import.
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[[image:DataImport.png|left|]]<br clear="all" />
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=== Import data to Cytoscape ===
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* To import the experimental data, select '''File > Import > Table from File...'''. Select the ''starvation_dataset_trans.txt'' file and click '''Open'''.
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* Under '''Where to Import Table Data''', choose '''To selected networks only'''.
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* To select both pathways, click the '''Select All''' button.
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* Under '''Key Column for Networks''', select '''XrefId''' (the column with Ensembl IDs).
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* In the '''Preview''' section, click the expand symbol at the top of the '''ensid''' column. This will open an interface where you can define the details of the column, such as data type etc.
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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.
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=== Identifier mapping with BridgeDb ===
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[[image:DataImport.png|600px|left|]]<br clear="all" />
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Since the data is annotated with Affymetrix probe set identifiers, it needs to be mapped to a standard identifier type to visualize it on pathways. The BridgeDb app does exactly this, given a mapping file. Before performing the mapping, we have to import the appropriate mapping file to BridegDb.
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* Open the BridgeDb app under '''Apps > BridegDb > Manage ID Mapping Resources'''.
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* Click '''OK''' to import the data.
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[[Image:BridegDb_Resources.png|left|]]<br clear="all" />
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= Data visualization on pathways =
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BridgeDb works with mapping information from various sources. For example, y ou can either download a database [http://www.pathvisio.org/downloads/download-bridgedbs/ here], and after extracting it you can select it under '''Databases''' in the '''ID Mapping Resouces Configuration''' interface. You can also supply a local or remote mapping file.
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The data and pathways are now both imported and linked and we can visualize the data on the pathways. For this tutorial, we will create a color scheme for all significant nodes, based on ANOVA values for a comparison across three experimental groups.
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For this tutorial, we will use Web Services for the mappings.
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* Click on the '''Web Services''' entry in the list of ID mapping sources.
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* In the '''Control Panel''' on the left side of Cytoscape, select the '''Style''' tab.
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* In the '''Webservice-based ID Mapping Resources Configuration''' interface, select '''BridegDb web service''' in the drop-down.
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* In the list of '''Properties''' click on the triangle next to '''Fill Color''' to expand.
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* Click on '''Fill Color''' next to Column. In the drop-down, select '''ANOVA''' to select the ANOVA column from the data.
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* Under '''MappingType''', select '''Continous Mapping'''.  
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[[Image:BridgeDb_webservice.png|left|]]<br clear="all" />
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[[image:ContinousDefault.png|left|]]<br clear="all" />
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* In the '''Base URL of BridgeDb web service''' drop-down, select the entry for mouse. Click '''OK''' to continue.
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* Double-click on the default color continuum to customize it.
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* Set the min/max values by clicking the '''Set Min and Max...''' button. Set Min to 0 and Max to 0.05.
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* Set the colors for both min and max by double-clicking on the small triangles and choosing a shade of green.
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* For the large right-most triangle, set the color to a pale gray color.  
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You will see a listing of supported ID systems, note that Affymetrix is listed. We are now ready to perform the mapping.
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You now have a color scheme where nodes with an ANOVA value of 0.05 or below is colored green, and all other measured nodes are colored gray. Nodes that are not found will simply be white.
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[[Image:BridgeDb_Config.png|left|]]<br clear="all" />
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[[image:PathwayViz.png|left|]]<br clear="all" />
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* Close the '''ID Mapping Source Configuration''' interface.
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=== Export visualizations ===
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* Select '''Apps > BridegDb > Map Identifiers'''.
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Any pathway or network visualization in Cytoscape can be exported into a number of graphical file formats, which can easily be included in publications and websites. File formats supported for export are PNG, JPEG, PDF, PostScript and SVG.  
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= Viewing data on pathways =
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* To export the pathway visualization, select '''File > Export > Network View as Graphics...'''
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* Select the export file format, and designate a location name filename for the export.
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=== Open WikiPathways in Cytoscape ===
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[[image:ExportPathway.png|left|]]<br clear="all" />
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=== Visual Styles ===
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-->

Current revision

This tutorial has been replaced by the WikiPathways App Tutorial.

Retrieved from "https://classic.wikipathways.org/index.php/Help:DataVisualizationInCytoscape"
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