GDC-TCGA/Xena Browser Data Differences

[Ashwin Mukund]

I was looking into HTseq RNA Gene Expression data (fpkm) GDC TCGA-LUSC data from the Xena browser, and I am trying to match the expression values there to the data on GDC TCGA-LUSC. I was able to match some of the sample ID's to the case ID's on the TCGA-LUSC page and download the STAR counts file containing Gene Expression Quantification information. Xena states that the FPKM values were log2 transformed, but when I try to match a gene value from Xena to a gene in the STAR counts file, using this transformation it does not work. Can someone validate whether I am looking in the correct place? Or are there additional data transformations in the Xena file that would allow me to match the data?

UCSC Xena (xenabrowser.net)

Cases (cancer.gov)

[Mary Goldman]

Hi Ashwin,

Our data from the GDC was last updated in 2019 so this is the reason you are seeing the discrepancy with our data and the most current data from the GDC. We are currently working to update our GDC data.

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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[Agustina Angeloni]

Is it for this reason also that the beta values of methylation in Xena browser have variations with respect to the beta values provided in the .txt to the GDC app? As I understand it , the Sesame package was after the publication of the Xena data... Thank you

[Mary Goldman]

Hi Augustina,

Yes, exactly. The files that we host are from 2019 and underwent different harmonization and processing than the files currently on the GDC.

Best,

Mar

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