Accessing and Processing Mature miRNA Data in TCGA BRCA Cohort

[Özge Yüksel]

Dear Xena Browser Team,

I am working on a differential expression analysis of mature microRNA (miRNA) expression levels for specific phenotypes in the TCGA BRCA cohort. I need to filter some samples according to their clinical states. While accessing the datasets through R, I have encountered numerous empty entries, causing issues in my analysis.

I understand that it is possible to reach the raw data through TCGA. However, I have been unable to find the mature forms of miRNAs identified by MIMAT IDs in the TCGA datasets. Could you please guide how you converted the TCGA data into the "TCGA.BRCA.sampleMap/miRNA_HiSeq_gene" dataset? Is the process you used available for public access?

Thank you for your assistance.

[Mary Goldman]

Hello,

Here is our dataset page for this data (https://xenabrowser.net/datapages/?dataset=TCGA.BRCA.sampleMap%2FmiRNA_HiSeq_gene&host=https%3A%2F%2Ftcga.xenahubs.net). You can also see the wrangling that we did on the data and where we originally downloaded the data form. Unfortunately, the place we originally downloaded this data is no longer available. The GDC hosted this data for a while in its archive but I am unsure if it is still hosting it. I would recommend going back to the original publication for this data to see how the data was processed. The GDC has a page for finding these publications here: https://gdc.cancer.gov/about-data/publications.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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