WikiPathways is a database of biological pathways maintained by and for the scientific community. Each pathway model in the database is annotated with database identfiers, which can be used for computation and data visualization. The WikiPathways App for Cytoscape is available from the App Store.
This tutorial includes a basic workflow for visualizing experimental data on pathways in Cytoscape, as well as how to import pathways as networks.
- Install and launch the latest version of Cytoscape.
- Install the WikiPathways app via Apps → App Manager.
- Download the experimental data.
The data is a lung cancer dataset from TCGA, comparing lung cancer biopses versus normal tissue.
- Launch Cytoscape, and in the Network Search Tool at the top of the Network tab in the Control Panel, select WikiPathways in the drop-down. Type in "cell cycle" (with quotes) and click the search icon.
- A list of results for all available species will open. To see results from a select species, click the Only checkbox and select a species from the drop-down.
- Select the human Cell Cycle and click Import as Pathway, or simply double-click the pathway in the list.
The pathway opens in Cytoscape with the original pathway layout and the WikiPathways style:
Pathway Node Identifiers
Nodes in pathways from WikiPathways are annotated with identifiers from public databases, visible in the XrefId column in the Node Table. During import, the WikiPathways App maps these identifiers automatically to Ensembl identifiers, adding them to a new column.
The experimental data in this case is annotated with Ensembl identifiers, so we can use the new Ensembl column to map to the data:
- Load the lung.expr.csv file under File menu, select Import → Table from File..... Alternatively, drag and drop the data file directly onto the Node Table.
- Under Where to Import Table Data, select To a Network Collection and select the relevant network collection in the second drop-down.
- In the Key Column for Network drop-down, select the new Ensembl column.
- In the Preview table, note that the Gene ID column is already selected as the key.
The data import interface should now look like this:
- Click OK to import.
- Once import is complete, look for the newly imported data columns in the Node Table to confirm that it worked.
Mapping Data to Visual Properties
We now have the data in Cytoscape, linked to the pathway, and ready to map to visual properties of the nodes in the network. We are going to visualize the fold change as Node Fill Color.
- In the Style tab of the Control Panel, click the Map. box for Fill Color.
- In the Column drop-down, select "log2FC".
- In the Mapping Type drop-down, select Continuous Mapping. This will create a default color gradient from blue (negative fold change) to red (positive fold change):
Importing Pathways as Networks
In addition to importing pathways with the visual style and layout unique to WikiPathways, the WikiPathways App also allows import of any pathway as a simple network.
- Again, select WikiPathways in the drop-down of the Network Search Tool and search for "cell cycle" (with the quotes) and click the search icon.
- In the list of results, select the human pathway and click Import as Network.
- We can now repeat the data import and style selection to create a visualization like in the previous pathway:
Downstream Analysis Options
Whether you import pathways as networks or as pathways, there are many different downstream analysis options available in Cytoscape:
Cytoscape provides a number of ways to export results and visualizations:
- As an image: File → Export → Network to Image...
- To a public repository: File → Export → Network to NDEx, or File → Export → Collection to NDEx
- As a Cytoscape JSON file: File → Export → Network to File and select Cytoscape.js JSON as the format.