Viewing Gene Networks in the cBio Portal

IGV connects to the cBio Cancer Genomics Portal to display information about networks of genes. An IGV gene list is used to provide seed genes to the cBio portal, which then displays a network of the seed genes and their neighboring genes. You can filter the network based on mutation, copy number, and expression data that you have loaded into IGV.

The following example illustrates how to use this feature in IGV.

1. Load mutation, copy number, and expression data from the The Cancer Genome Atlas (TCGA) glioblastoma study available from File>Load From Server:

  • Select the Human hg18 genome from the genome drop-down menu.
  • Select File>Load From Server.
  • Open The Cancer Genome Atlas and click on the checkbox to select GBM Subtypes (Verhaak et. al.).
  • Click on OK to load the data.

2. Specify the seed genes and retrieve network information from the cBio Portal:

  • Open the Gene List Manager by selecting Regions>Gene Lists.
  • Select a gene list or define a new one.  
  • Click Retrieve Network

                                                                     

3. IGV displays the network information first in tabular form.

  • Each row in the table represents a gene in the network; the seed gene names are displayed in bold.  
  • The first column after the gene name shows how many connections the gene has in the network.
  • Subsequent columns indicate the fraction of the loaded samples that are "altered" at that locus. The alterations are based on data values in the following categories: mutation, copy number amplification/deletion, and gene expression up/down regulation.

4. Configure the network.

  • You can reduce the network by eliminating genes that do not pass certain filter criteria based on the alteration values. Click the "+" and "-" buttons in the Filter tab to add and remove criteria. Note that seed genes are never filtered out.
  • Filters are based on the percentage of samples that show a given alteration in a given gene. You can set the values that define the alteration in the Thresholds tab. For instance, if 10% of samples had 2 mutations in a given gene, 20% had 1 mutation, and 70% had no mutations, then setting the mutation threshold to 1 would yield a "Percent Mutated" value of 30. If a mutation filter existed, it would need to have a minimum below 30 and a maximum above 30 to include this gene.
  • From the Seed Genes tab you can edit the list of seed genes and retrieve a new network; there is no need to go back to the Regions>Gene List window if you want to adjust the list. 

5. View the network graph.

  • Once you have configured the network, click View Network in the Filter tab.
  • This opens a web browser and shows the cBio Network Viewer, with the network of genes you have selected, color-coded by the sample data loaded.
  • Controls in this viewer allow you to further configure the network display and layout. This is documented in the Help tab in the right panel of the viewer.  
  • Note: To view the cBio network graph, make sure that your web browser settings do not disable JavaScript.