Cbio help

[Chen, Joyce]

Good morning!

I have a couple of questions need your help.

1. How to compare two virtual groups? I have curated and defined two virtual groups (19PDM and CMM), and would like to compare survival, mutation profile and CNVs. What is the best way to combine those two into one cohort in Cbio?
2. Does Cbio offer the disease free survival curve?
3. If I were to use the figures for publication, how do I cite cBio and describe the statistical analyses?
   
   
   Thank you!  

Joyce Chen MD, PhD

Dermatopathology Service

Department of Pathology and Laboratory Medicine 

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[Guizela Huelsz Prince]

Hi Joyce,

1. Comparing Groups: You can find a step-by-step guide in these slides. Briefly, you first need to save your defined groups using the "Groups" button in the top-right section of the Study View. Once saved, you can select both groups and click the "Compare" button to enter the Comparison View, where you can analyze survival, mutations, and CNVs side-by-side.

2. Disease-Free Survival: cBioPortal does offer these curves, but their availability depends entirely on whether the underlying study contains that specific clinical data. If available, they are visible in the Study View.

3. Citations: Information on how to cite cBioPortal can be found here: https://docs.cbioportal.org/user-guide/faq/#how-do-i-cite-the-cbioportal

Let me know if you have any more questions!

Best,

Guizela

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[Chen, Joyce]

Hi Guizela,

Thank you for the detailed reply!

For the first question, I actually meant how to compare two different virtual studies (19PDM and CMM), rather than comparing different groups within a single virtual study. The issue I’m running into is that when I select both virtual studies and then click “Explore Selected Studies,” the previously defined cohorts in each study disappear. Could you please help with this?

For the second question, I’ve only seen overall survival curves so far. Could you show me a few examples of cancer‑free survival curves within the Study View? Also, is it possible to generate cancer‑free survival curves based on the existing overall survival?

3. Those references are very helpful. Is there a summary of all the statistical analyses used by cBioPortal, since all the figures it generates include a p‑value?

Many thanks,

Joyce Chen MD, PhD

Dermatopathology Service

Department of Pathology and Laboratory Medicine 

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From: Guizela Huelsz Prince <gui...@se4.bio>
Sent: Friday, March 13, 2026 6:42 AM
To: Chen, Joyce <Che...@mskcc.org>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: [EXTERNAL] Re: [cbioportal] Cbio help

 

[Guizela Huelsz Prince]

Hi Joyce,

1. Thanks for the clarification, I see how this can be tricky. A workaround is to re-define your groups using Sample IDs once you have both studies open. Here is the most efficient way to do that:

1. Get your Sample Lists:

• Open your 19PDM virtual study.

• In the Study View, click the "Custom Selection" button (top right), then click "Currently Selected." This will populate the text box with all sample IDs in that study. Copy this list.

• Repeat this for the CMM virtual study and save that list separately.

  

2. Combine the Studies:

• Now, select both virtual studies from your dashboard and click "Explore Selected Studies."

3. Re-create the Groups:

• While viewing the combined studies, click "Custom Selection" again.

• Paste the 19PDM list into the box and click "Filter to listed samples."

• With those samples filtered, click the "Groups" button (top right) and select "Save selection as group." Name it "19PDM."

• Click "Clear All" filters, then repeat the process for the CMM list.

4. Compare:

• Once both are saved as groups within this combined session, select them both in the Groups menu and click "Compare."

2. You can look at the Breast Invasive Carcinoma (TCGA, PanCancer Atlas) study for an example of both Disease-Free and Overall Survival curves. Because they track different clinical events (recurrence/progression vs. death), cBioPortal cannot "generate" one from the other; both require their own specific data points to be present in the original study.

3. I don't think there is a single place where all statistical analyses are described. For group comparison specifically, you can see which tests are performed for the different plots: https://docs.cbioportal.org/user-guide/faq/#what-are-the-statistical-significance-tests-in-group-comparison. If you can't find information for a specific plot, let me know and I can help you figure it out.

Best,

Guizela