Entrez ID of 0 issue

[Joseph, Greg]

Hello,

 

We have Whole Transcriptome data that we are uploading for the expression data. We utilize the Z-score normalization script and referenced the gene list for the panel to extract Entrez IDs, but there are many regions that have an Entrez ID of 0, which the import script does not like. I recall seeing similar issue on the discussion board but was unable to find the thread. Any recommendations on how to resolve this import error?

 

 

Thanks,

Greg Joseph

[Benjamin Gross]

Hi Greg,

For clarity, are you working with your own curated dataset and are missing Entrez IDs for a number of symbols used in your panel / expression file?  Can you resolve the ids by using the symbol and help from a site like genenames.org?

Regards,

Benjamin

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[Joseph, Greg]

Hi Benjamin,

 

Yes, your clarification is our exact situation. We have 1,973 gene symbols which do not have corresponding Entrez IDs. Any insight on how best to address this issue is greatly appreciated.

 

Thanks,

Greg

[su...@mskcc.org]

Hi Greg,

By leaving the entrez ID field empty, or simply delete the column should resolve the import error. 

Please let us know if there are still issues.

Regards,

Yichao

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From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Joseph, Greg <gregory.ja...@emory.edu>
Sent: Friday, December 10, 2021 11:26 AM
To: Benjamin Gross <benjami...@gmail.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: RE: [External] Re: [cbioportal] Entrez ID of 0 issue

 

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[Marcus Kelly]

This seems to be a very broad issue with the current data release-- I have just downloaded the TCGA BRCA pan-cancer atlas data, and every mutation has an Entrez_Gene_Id of 0. Given that Entrez is a more stable means of identifying genes, this seems to be a pretty critical issue...

[Yichao S]

Hi Greg,

Thanks for spotting this. We've adjusted our pipeline and are re-annotating all the MAFs for pancan studies now, and this will fill the entrez IDs back.

I've logged the issue here (https://github.com/cBioPortal/datahub/issues/1640) and you can track our progress for the reannotation here.

Regards,

Yichao

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