GTEx expression in UCSC and in their official GTEx page differs

[Mozere, Monika]

Hello,

I have a question about the expression data from GTEx and the differences I see between values in UCSC genome browser vs GTEx official website.

For each gene I find a different value of RPKM in UCSC vs GTEx web page.  for example: gene WASH7P is reported to have a 6.9 RPKM in adipose-subcutaneous in UCSC but 8.3 RPKM in the same tissue in GTEx official website. The same with all other genes.

Would you know why do we see those discrepancies? Both websites report that they use the same V6 version.. I would expect to have the same values for each gene.

Thanks,

Best Wishes,

Monika

[Luvina Guruvadoo]

Hello Monika,

Thank you for your question. The GTEx portal recently updated to a slightly newer version than we host (see release notes below). This explains the expression level differences from our site.

2016-9-9
V6p Data Released
The GTEx Portal has been updated with a patch release for V6 (dbGaP accession phs000424.v6.p1), called V6p. This release provides new gene-level expression quantifications and eQTL results based on an improved gene-level annotation derived from GENCODE v19. All data from this release are available for download from the GTEx Portal.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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