downloading expression and mutation data

[Soheil Shams]

Dear Team,

 

Congratulations on a very nice tool. I am exploring the TCGA data and can’t find two functions that I think you have but not easy for me to find.

1. I would like to get the mRNA expression normalized data for all genes (or the top highest and lowest expressed) for a group of samples. I can see the selection but can’t see the expression profiles:

 

2. I would like to get a table for all the samples showing which genes are mutated. Is there anyway of getting this.

 

Thanks a lot

 

Soheil

 

[Prasanna Jagannathan]

Hi Soheil

Thanks for using cBioPortal effectively. Glad it helped in your work.

It is possible to select the charts required from the "charts" popup by clicking the "charts" button. In the "Gene Specific" tab, the options to select the various mRNA data are available. The list of genes have to be entered in the Gene list. On clicking the "Add Chart" button all charts will appear below. Please see the screenshots below.

The entire dataset is available at the below link. There are options to download the original data as well. Please see the screenshot.

https://cbioportal-datahub.s3.amazonaws.com/coadread_tcga_pan_can_atlas_2018.tar.gz

thanks

Jag

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[Soheil Shams]

Dear Jag

 

Thank you for the helpful reply.

 

Best regards

Soheil

 

From: Prasanna Jagannathan <jagn...@gmail.com>
Sent: Tuesday, April 8, 2025 8:24 AM
To: Soheil Shams <ssh...@tesa-research.com>
Cc: cbiop...@googlegroups.com; Klaudia Pacewicz <kla...@tesa-research.com>
Subject: Re: [cbioportal] downloading expression and mutation data

 

Hi Soheil

 

Thanks for using cBioPortal effectively. Glad it helped in your work.

 

It is possible to select the charts required from the "charts" popup by clicking the "charts" button. In the "Gene Specific" tab, the options to select the various mRNA data are available. The list of genes have to be entered in the Gene list. On clicking the "Add Chart" button all charts will appear below. Please see the screenshots below.

 

 

 

 

 

 

The entire dataset is available at the below link. There are options to download the original data as well. Please see the screenshot.

https://cbioportal-datahub.s3.amazonaws.com/coadread_tcga_pan_can_atlas_2018.tar.gz

 

 

 

 

 

 

thanks

Jag