GTEX TCGA new recompute available?

[Donogh O'Brien]

Hi Mary

hope this finds you well.

Dannenfelser et al, 2020 ( PMID: 32916097) appear to have recomputed RNAseq data to compare 11,057 TCGA tumours with 10,429 GTEX normal tissues (GTEX release 7) which is the basis of their web tool Antigen Explorer.

This is an increase in the GTEX data compared to the Toil recompute in the TCGA/Target/GTEX dataset at Xena. This may be important because there are some differences comparing tumour versus normal using Xena or AE. For example EPCAM shows highest expression in cancer (Xena) but normal esophagous and colon in AE.

Would it be possible to add the Dannenfelser dataset to the list of Xena datasets available?

Best wishes

Don

[Mary Goldman]

Hi Don,

It would be great to have a more updated GTEx dataset! Thanks for bringing this to our attention.

If you can point me to where the sample-by-gene matrix (single file for both TCGA and GTEx together) is located then we can upload it into a data hub, likely some time in October.

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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[Donogh O'Brien]

Hi Mary

I'm afraid they don't make these files available; you have to use their site Antigen Explorer (AE)with very limited download possibilities. On close insprection I much prefer the read out from the Toil recompute which shows common tumour associated antigens like EpCam with the highest expression in cancer compared to normal tissues; AE shows the opposite and  suggests that most common TAAs have highest expression in normal samples which doesn't make sense to me.

Best wishes

Don

[Mary Goldman]

Hi Don,

Too bad the download possibilities are so limited. And good to know about the TAAs. Thank you as always for reaching out.

Best,

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