ENST IDs

[Jacob Neumann]

Hello,

I am concerned about the accuracy of the Ensembl IDs used in my comparison of transcript samples between GTEx and TCGA datasets. A significant number of Ensembl transcript IDs that appear in my results do not seem to exist in the current Ensembl database. I would like to understand whether these IDs are outdated, deprecated, or if there’s an issue with the dataset annotations I am using. Can you clarify why this discrepancy occurs and how to ensure I’m working with valid, up-to-date transcript information?

[Mary Goldman]

Hi Jacob,

The TCGA-GTEx dataset was generated in 2017 using Gencode v23. At this point in time the data providers have no plans to update this data. You can read more about this dataset here: https://xenabrowser.net/datapages/?host=https%3A%2F%2Ftoil.xenahubs.net

Best,

Mary

-----

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

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

--
You received this message because you are subscribed to the Google Groups "UCSC Xena and Cancer Genomics Browser" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ucsc-cancer-genomics...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/87008b58-1c66-4c5f-9900-486ffe2c76b9n%40googlegroups.com.