order of expScores in gtexGene table output

[I-Hsiu Lee]

Hi UCSC Genome Bioinformatics Staff,

The last column of the gtexGene table (https://genome.ucsc.edu/cgi-bin/hgTables) is a list of 53 expScores, one for each tissue in the database.  Should I assume that the order of the 53 scores and the corresponding tissues is the same as those in the x-axis of the figure "GTEx RNA Integrity by Tissue" near the bottom of the web page?

Thank you very much for the great jobs you do!

Best,

I-Hsiu Lee

[Cath Tyner]

Hello I-Hsiu,

Thank you for using the UCSC Genome Browser and for inquiring about the ordering of expScores as they relate to GTEx tissues. You are correct,

​our engineers have confirmed that ​

the 53 expScores are in the same ordering as (and correspond to) the tissues in the x-axis of the UCSC Genome Browser figure, "GTEx RNA Integrity by Tissue."

For example, for ENSG00000175164.9 (ABO), the 1st espScore listed is 0.165 and corresponds to "Adipose - Subcultaneous" while the last score, 0.075, corresponds to "Whole Blood."

I have created a bar chart of the raw expScores for ABO (ENSG00000175164.9) as an example. Comparing expScores to the transformed scores in the GTEx chart, you can see that the variability correlates to the same order in the X axis of the GTEx chart, as seen here.

Please note from the

​m​

ethods section of the GTEx track description page that "UCSC obtained the gene-level expression files, gene annotations and sample metadata from the GTEx Portal Download page.

​ ​

Median expression level in RPKM was computed per gene/per tissue."

Please respond to this list if you have further questions!

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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