[cbioportal] Uploading public data

[HIROMI YANASE]

Dear cBioPortal team,

 

I tried to import the MIR-218-1/218 gene data, but the error below appeared.
Could you please tell me how to resolve this error?

 

 

Thank you for your continued support.

 

Regards,

Hiromi

 

------------------------------------------------------
Hiromi Yanase

Evidence Generation Department

Medical Affairs Division

 

KONICAMINOLTA REALM, INC.

Hamamatsucho Bldg.

1-1-1 Shibaura, Minatoku,Tokyo 105-0023,JAPAN

Tel:+81 3-6324-1023

E-mail:hiormi...@konicaminolta.com

-------------------------------------------------------

 

[jagn...@gmail.com]

Hi Hiromi

Please reply only to cbiop...@googlegroups.com

Just to clarify, are you planning to upload patient data with the gene below to a public study in cbioportal.org website?

https://www.ncbi.nlm.nih.gov/datasets/gene/id/407000/

https://www.ncbi.nlm.nih.gov/gene/407000/

Please reply only to cbiop...@googlegroups.com

thanks

Jag

[HIROMI YANASE]

Hello Jag and cBioPortal team,

 

Thank you for your e-mail.

Yes, I tried to upload the patient's mRNA expression data for MIR218-1, which you shared via the link, to cBioPortal.

However, since the gene symbol MIR218-1 is considered invalid in cBioPortal,

I converted the gene name to MIR218-1-1/218 and attempted to upload the data, but an error occurred.

 

 

Regards,

Hiromi

 

 

From: jagn...@gmail.com <jagn...@gmail.com>
Sent: Tuesday, June 10, 2025 2:26 AM
To: HIROMI YANASE <hiromi...@konicaminolta.com>
Subject: [External] Private message regarding: [cbioportal] Uploading public data

 

Hi Hiromi

Please reply only to cbiop...@googlegroups.com

Just to clarify, are you planning to upload patient data with the gene below to a public study in cbioportal.org website?

 

https://www.ncbi.nlm.nih.gov/datasets/gene/id/407000/

https://www.ncbi.nlm.nih.gov/gene/407000/

 

Please reply only to cbiop...@googlegroups.com

 

thanks

Jag

 

On Friday, 6 June 2025 at 7:50:27 am UTC-4 HIROMI YANASE wrote:

Dear cBioPortal team,

 

I tried to import the MIR-218-1/218 gene data, but the error below appeared.
Could you please tell me how to resolve this error?

 

 

Thank you for your continued support.

[Prasanna Jagannathan]

Hi Hiromi

If you want to upload to cbioportal.org, (public data available on cbioportal.org website), the process is to connect with the cBioPortal Data Hub team with the dataset and publication. We would need the link to the publication. The cBioPortal data hub team will import the study data.

Here is an example query of the Whole Genome study which has the genes of interest to you.

https://www.cbioportal.org/results/oncoprint?cancer_study_list=pancan_pcawg_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Ccna&case_set_id=pancan_pcawg_2020_cnaseq&gene_list=MIR-218-2%252F2*%2520MIR-218-1%252F1*&geneset_list=%20&tab_index=tab_visualize&Action=Submit

If you want to upload to your own private cbioportal instance,

Please check if the gene is available in your cBioPortal database instance.

The following documentation steps could help.

https://docs.cbioportal.org/import-gene-panels/#import-gene-panels 

https://docs.cbioportal.org/updating-gene-and-gene_alias-tables/#updating-the-gene-names-and-aliases-tables

thanks

Jag

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[HIROMI YANASE]

Hello Jag,

 

Thank you for your support.

I’ll try to upload the data to my private cBioPortal.

 

Regards,

Hiromi