Re: [cbioportal] TCGA dataset question

[debr...@mskcc.org]

Dear Dr Benej,

 

Thanks for reaching out! Apologies about the delay in getting back to you

 

For the TCGA PanCancer datasets we don’t have the expression miRNA loaded yet. We have an open ticket to add this:

 

https://github.com/cBioPortal/datahub/issues/241

 

Note that for the published TCGA studies we do have some miRNA expression loaded. See e.g. this query:

 

https://www.cbioportal.org/results/coexpression?cancer_study_list=gbm_tcga_pub&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mrna_median_Zscores&case_set_id=gbm_tcga_pub_mrna&gene_list=MIR-210%252F3P&geneset_list=%20&tab_index=tab_visualize&Action=Submit

 

If you select the microRNA expression profile you can see the expression data for this TCGA study. On the datasets page you can find which other studies have miRNA data available:

 

https://www.cbioportal.org/datasets

 

Click on columns > Tumor miRNA. Then sort by the new column that shows up by clicking on it

 

Hope that helps! Please reach out if you have more questions

 

Best wishes,

Ino

 

From: "'Benej, Martin' via cBioPortal for Cancer Genomics Discussion Group" <cbiop...@googlegroups.com>
Reply-To: "Benej, Martin" <Martin...@osumc.edu>
Date: Thursday, December 30, 2021 at 2:21 PM
To: "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] TCGA dataset question

 

Good afternoon,

We are browsing through the TCGA curated PanCancer datasets and found one particular gene of interest, miR-210/3p, whose expression is missing from all the datasets. There is mutation, structural variation and copy number data available for this gene an its other forms (miR210/210 and miR210/5p) but not mRNA or protein expression.

Is there any way to recover these data? Or a particular reason why this particular gene is not present in any of the expression datasets?

Thank you in advance.

Best,

Martin

 

Martin Benej, PhD
Post Doctoral Researcher
The Ohio State University Wexner Medical CenterDepartment of Radiation Oncology
#344 Tzagournis Medical Research Facility, 420 W 12th Avenue, Columbus, OH, 43210
(614) 685-5844 Office
martin...@osumc.edu

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