mRNA profile not available

[Franz Ketzer]

Hi,

 

first of all, I’m a big fan of your work, the portal is brilliant.

Unfortunately, I’ve repeatedly encountered the same issue with querying patients subpopulations according to mRNA expression. Even though mRNA expression data is available in the data set, cBioPortal tells me that is not available for querying with OQL. Can you provide a workaround or fix this potential bug?

Best,

Franz

 

Dr. Franz Ketzer

Institute for Clinical Chemistry and Pathobiochemistry

TUM Klinikum Rechts der Isar

+49894140-9124

 

[Aaron L]

THanks for the report Franz, we're looking.

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[Aaron L]

Franz, 

What I've found so far is that some molecular profiles (in this case the expression profile you are interested in) are deliberately excluded from analysis tool.  There's a flag in the database.  The data can be downloaded, but not analyzed.  I'm inquiring into the general reasons why this might be the case.  Could be different for different studies.   But it's a feature.

--Aaron 

[JJ Gao]

Hi Franze,

Thanks for letting us know. This looks like data bug. We are looking into it: https://github.com/cBioPortal/datahub/issues/2263

Best,

-JJ

On Tue, Feb 10, 2026 at 12:01 PM Aaron L <lisman...@gmail.com> wrote:

@JJ Gao can you comment?  lets first see if there was a good reason to exclude the data from analysis or if i was a mistake.

On Tue, Feb 10, 2026 at 11:44 AM Franz Ketzer <franz....@tum.de> wrote:

If this doesn’t work, is there another way to check Survival of high and low expressing patient cohorts for a certain gene in these data sets?

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Von: Aaron L <lisman...@gmail.com>
Gesendet: Dienstag, Februar 10, 2026 4:34 PM
An: Franz Ketzer <franz....@tum.de>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Betreff: Re: [cbioportal] mRNA profile not available

 

[Ramya Madupuri]

Hi Franz,

Thank you for catching that! The profile is now available for you to query. Can you give it another try?

Best,

Ramya

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/CABbxrZNvHJC7vUYSivwSt6iQ%3DYjTzihY%2BWW4kfvXh_yU5FZQ3g%40mail.gmail.com.

[Ramya Madupuri]

Hi Franz, 

Yes, we have identified that a few studies were mistakenly excluded from the query results. A broader fix is currently in progress to address this across affected studies at https://github.com/cBioPortal/datahub/issues/2263.

Thank you,

Ramya

On Thu, Feb 12, 2026 at 2:57 AM Franz Ketzer <franz....@tum.de> wrote:

Hi,

 

yes, it works now for the Fraser study I sent you. However, it doesn’t work for other studies, like this one:

 

Maybe it’s a general issue? Thanks for your help!

[Aaron L]

Hi Franz, 

Let me know if you are still blocked and I can help while fix is put in place.

--Aaron

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/CAOk5JipoF%3DhV%3DH6uo8Lsqmf_wr40qFEsp3ZL2tjEnH%3DJwXjFFA%40mail.gmail.com.

[Franz Ketzer]

Hi,

Thank you, it seems to be working now! 

Appreciate your help.

Best,

Franz

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Von: Aaron L <lisman...@gmail.com>
Gesendet: Donnerstag, Februar 19, 2026 5:41 PM
An: Ramya Madupuri <ramyama...@gmail.com>
Cc: Franz Ketzer <franz....@tum.de>; cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>