cBioPortal Tutorial #4:
Virtual Studies
Create and save your own custom study comprised of samples from existing studies
Last update: December 23, 2021
Tutorial Objectives
Virtual Study Overview
What is a Virtual Study?
A virtual study is a custom study comprised of samples from one or more existing studies.
Why is a virtual study useful?
The virtual study feature allows you to define a custom cohort of samples that fit your specific genomic or clinical criteria of interest. These samples can be a subset of the data available in an existing study, or result from the combination of multiple existing studies. This cohort of samples can then be queried or explored just like a traditional study, and can be returned to at a later date or shared with a collaborator.
In this tutorial, we will create a virtual study comprised of a subset of samples from two existing TCGA glioma studies.
We begin by selecting the studies of interest and viewing them in the Study Summary page.
Creating a virtual study: Selecting studies
1. Use the search box to find the studies of interest
2. Select the studies of interest
3. Click “Explore Selected Studies”
Link to this page
Creating a virtual study: Study summary page
Click on the to see the list of studies
This is the same Study Summary page that you see for a single study, but now with data from 2 studies.
Link to this page
Creating a virtual study: Study summary page
Use this table to select samples with IDH1 mutations
(Click the check box in the “#” column, then “Select Samples” at the bottom of the table)
In this example, we will additionally filter to samples with mutations in IDH1.
Link to this page
We are now ready to create our virtual study.
What you see will differ slightly depending on if you are logged in or not. The next two slides show what the virtual study button looks like in each scenario.
Virtual study button (not logged in)
Enter a name for your virtual study (optional)
Click on the link to open your virtual study, or click “Copy” to copy the URL to your clipboard.
Text box pre-filled with a description of the studies contributing samples and filters applied to the samples. You can edit this text.
List of studies contributing to samples with links to the study summary for each
Click here to create and share your virtual study
Link to this page
Virtual study button (logged in)
When you save a study, it is added to the homepage, at the top of the study list under “My Virtual Studies”. Clicking “Query” brings you to the query selector with your new virtual study pre-selected.
The “Save” button only appears when you are logged in.
The “Share” button works exactly the same as when not logged in
Link to this page
Whether or not you are logged in, let’s continue
on to view this new virtual study.
Virtual study: Study summary page
We can now see the study summary page for our newly created virtual study. You can now explore these samples or run a query, just like with a traditional study.
Remember that while making this study we filtered down to IDH1 mutant samples, but the non-mutant samples were still present. Now, those samples without mutations are completely gone.
Click on the to see the description of this virtual study
Link to this page
Logging in to cBioPortal:
If you use a private instance of cBioPortal, you might already go through an authentication process (through your university, for example). If so, there is nothing else you need to do.
But if you don’t normally log in, then let’s go through how this works.
Logging in
Link to this page
Click here
Logging in
We use Google and Microsoft for authentication. Sign in with any Google or Microsoft account.
Logging in
Link to this page
your email address
Here’s the virtual study I made
This is what you see when you log in
Virtual Study Authentication Questions
Is it necessary to log in to use virtual studies?
No. A user that has not logged in can create virtual studies and run queries in those studies (by using the query box on the study summary page). Links to virtual studies are permanent, so you can save the link on your computer and come back to it anytime, or share it with others.
If I do log in, what additional functionality do I gain?
If you log in, you gain the ability to save your virtual study to the list of existing studies on the homepage. This makes a virtual study functionally the same as any other study: you can access your virtual studies in the query builder and you can combine an existing virtual study with any other study to create a new virtual study.
Questions?
Check out our other tutorials
or email us at: cbioportal@googlegroups.com