Gene Ontology Term Data Visualization

Cytoscape is an open source software platform for integrating, visualizing, and analyzing measurement data in the context of networks.

This protocol includes a basic workflow for visualizing experimental data on a Gene Ontology term of interest in Cytoscape:

• Retrieve genes associated with a GO term
• Retrieving relevant interactions from public databases
• Integration and visualization of experimental data
• Exporting network visualizations

Setup

• Install the stringApp via Apps → App Manager.
• Download the experimental data (follow the link and on the page, right-click and select Save As...).
  
  The data is a lung cancer dataset from TCGA, comparing lung cancer biopses versus normal tissue.

Retrieveing Gene Ontology Term Genes

From enrichment analysis, we know that some Gene Ontology Biological Process terms are enriched in this data. We will choose one of these terms for visualization, GO:1902850; microtubule cytoskeleton organization involved in mitosis.

• Go to the AmiGO browser and search for GO:1902850 using the Quick search field.
• On the results page, click the link for genes and gene products. This will show associated genes for all organisms.

Retrieveing Gene Ontology Term Genes

• On the left side, click Organism to expand and then click the green plus sign next to Homo sapiens. At the top of the gene list, the number of Total gene products should now be around 148.
• Click the Custom DL button. In the popup, drag the top entry, Gene/product (bioentity), to the left, to exclude it from the download. Click Download.
• On the page that opens, select and copy the list of gene symbols. It is also a good idea to save the list by pasting it into any text editor.

Retrieve Interactions from STRING

We can now use the list of gene symbols for the GO term to search the STRING database.

• Launch Cytoscape. In the Network Search bar at the top of the Network Panel, select STRING protein query from the drop-down, and paste in the list genes.
• Open the options panel and confirm you are searching Homo sapiens, change the Confidence cutoff to 0.80 and set 0 Maximum additional interactors.
• Click the search icon to search. If any of the search terms are ambiguous, a Resolve Ambiguous Terms dialog will appear. Click Import to continue with the import using the default choices. The resulting network will load automatically.

STRING GO Term Network

The resulting network represents genes associated with the GO term, recognized by STRING, and interactions between them with an confidence score of 0.8 or greater.

Data Integration

Next we will import the data to create a visualization.

• Load the downloaded lung.expr.csv file under File menu by selecting Import → Table from File..... Alternatively, drag and drop the data file directly onto the Node Table.
• Select the display name column as the Key column for Network and select the GeneName column as the key column by clicking on the header and selecting the key symbol.
• Click OK to import. Two new columns of data will be added to the Node Table.

Visualization

Next, we will create a visualization of the imported data on the network. For more detailed information on data visualization, see the Visualizing Data tutorial.

• Go to the STRING Results Panel to the right of the network and uncheck Glass ball effect and STRING style colors. This will make the nodes
• Set the default Border Width to 2, and make the default Border Paint dark gray.
• Set the default node Label Font Size to 14.

Visualization

• For node Fill Color, create a continuous mapping for Log2FC.
• Save your new visualization under Copy Style... in the Options menu of the Style interface, and name it de genes up.
• Looking at only the largest connected component of the network (ignoring unconnected nodes), the network now looks like this:

Layout

We can change the layout of the network to see if we can improve the visualization.

• Apply the Prefuse Force Directed layout by clicking the Apply Preferred Layout button in the toolbar. The network will now look something like this:

Layout

The network has a highly connected group of nodes that appear to be upreuglated. We can alter the layout settings slightly to increase the readability:

• Select Layout → Settings to open the Layout Settings dialog.
• Make sure Prefuse Force Directed Layout is selected in the drop-down at the top. Change the Default Spring Length to 80. Click Apply Layout.

Exporting Networks

Cytoscape provides a number of ways to export results and visualizations:

• As an image: File → Export → Network to Image...
• To NDEx: Click the NDEx button in the toolbar and select Export Network to NDEx. Alternatively, select 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.