Expression levels and survival

[Zoe Angel]

Hi,

I am using cBioPortal and I have made a survival plot for my gene of interest in breast cancer studies.

Can I restrict the analysis to expression level only, like a KMplotter plot, or can I only have "unaltered" and "altered" as my groups? I would like to see if my gene is associated with GOF or LOF changes.

Any help would be much appreciated.

Many thanks,

Zoe

[Tali Mazor]

Hi Zoe,

I'm not familiar with KMplotter, but if I understand correctly, you want to compare outcomes for samples with high or low expression in a gene? If that's the case, there are multiple ways you can do this with cBioPortal. One option is to use OQL to run a query where your 'altered' samples will be defined based on mRNA expression z scores - see this video for an example: https://www.youtube.com/watch?v=kHlFXw2TMzc Or, you can define groups in study view based on mRNA expression levels and compare those groups - see this video for an example: https://www.youtube.com/watch?v=HTiKUXk0j0s

I hope that helps! If not, can you please clarify what you're trying to do?

-Tali

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[Zoe Angel]

Thanks so much Tali, I will try that. 

Many thanks! 

Zoe

---

From: Tali Mazor <tma...@ds.dfci.harvard.edu>
Sent: Friday, March 18, 2022 8:40:46 PM
To: Zoe Angel <C.A...@qub.ac.uk>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Expression levels and survival

 

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