"Hugo symbols not known to cBioPortal" error that shouldn't be

[Joseph, Greg]

Hello,

 

I am working to resolve some warnings in our dataset during import of a study to a local instance of cBioPortal. This question relates to the import step for data from Whole Transcriptome Sequencing data (RNA-Seq). We are using the first column as Hugo Gene Symbol and during data validation, the import.py script returned a warning that 16 of the Hugo Gene Symbols are “not known to cBioPortal”.

 

 

As a pre-processing step, I filtered the Hugo symbols in our data_expression.txt file to only be those symbols which exist within the “gene” table of the cBioPortal MySQL database, so this warning makes no sense. I have attached a screenshot of the 16 genes identified as “not known to cBioPortal” existing within the backend table.

 

Any insight on how to resolve this issue?

 

Thank you,

Greg

 

[Benjamin Gross]

Hi Greg,

I’m guessing you are using the metaImport.py script to import your data (https://docs.cbioportal.org/using-the-metaimport-script/)?  Is it possible you have it pointing to a different cBioPortal webservice (and database) than the instance you are importing into?

Best,

-Benjamin

On Jan 25, 2023, at 4:22 PM, Joseph, Greg <gregory...@emory.edu> wrote:

Hello,

 

I am working to resolve some warnings in our dataset during import of a study to a local instance of cBioPortal. This question relates to the import step for data from Whole Transcriptome Sequencing data (RNA-Seq). We are using the first column as Hugo Gene Symbol and during data validation, the import.py script returned a warning that 16 of the Hugo Gene Symbols are “not known to cBioPortal”.

 

<image001.png>

 

As a pre-processing step, I filtered the Hugo symbols in our data_expression.txt file to only be those symbols which exist within the “gene” table of the cBioPortal MySQL database, so this warning makes no sense. I have attached a screenshot of the 16 genes identified as “not known to cBioPortal” existing within the backend table.

 

Any insight on how to resolve this issue?

 

Thank you,

Greg

 

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