Entrez gene id not known to the cBioPortal instance

[Ji Hen Lau]

Hi,

I'm getting " Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id.  " warning during data validation of my CNA data, which suggests my gene reference data may be outdated or incomplete.

I've tried matching against gene_info.txt from the data curation tools on cBioPortal GitHub, but still encountering recognition issues with what appear to be valid current gene IDs/symbols.

Question: Does this meant I need to update my cBioPortal instance with the latest gene reference data, or can I somehow add missing genes to the existing gene database?

Since ignoring these genes will have about 10% of my data being dropped, so I wish that I could keep these data.

Any guidance on the proper procedure to refresh or supplement the gene reference data would be appreciated.

I deployed cBioPortal v6.2.0 via Docker on 22nd May 2025, following the guide. 

Thanks!

Regards,

Ji Hen

[Guizela Huelsz Prince]

Hi Ji Hen,

You can try generating your own gene database following some of the steps outlined here: https://docs.cbioportal.org/updating-gene-and-gene_alias-tables/

Cheers,

Guizela

[Ji Hen Lau]

Hi,

Thank you for reply, I will try it out. 

In the meantime, I would like to ask, in the case of:

Listing all values for the message: Entrez gene id exists, but gene symbol specified is not known to the cBioPortal instance. The gene symbol will be ignored. Might be wrong mapping, new or deprecated gene symbol.

Are these gene still being loaded, but with a different gene symbol that linked to the Entrez gene id? 

Regards, 

Ji Hen

[Guizela Huelsz Prince]

Hi Ji Hen,

Yes, if the entrez id is found, the data should be loaded. But the symbol that will displayed in the portal is the one listed in the second column of gene_info.txt. In this table, you can look up the cBioPortal-compatible symbols for some of the examples for which you get the warning, and double check if the genes are actually displayed in the portal when you query them using the new symbol.

Cheers,

Guizela

[Ji Hen Lau]

Thank you for the clarification !