Question: How to estimate significance of RPKM value on GTEX
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gravatar for GabrielMontenegro
4 months ago by
United Kingdom
GabrielMontenegro330 wrote:

After conducting a GWAS I have a set of SNPs and a set of genes that were significantly associated to my trait.

I want to know if the genes that I have found are significantly expressed on the tissues present in the GTEX database. I have never worked with expression data before, and I don't even know if talking about significance makes sense here.

For instance, say I want to know if BRCA2 is expressed in any of the tissues in the GTEX database. After querying the gene, what threshold value, based on this plot should I use?

Link for the search: https://www.gtexportal.org/home/gene/BRCA2

Thank you.

rna-seq expression gene • 244 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by GabrielMontenegro330

Reading the GTEX Science paper (http://science.sciencemag.org/content/348/6235/648/tab-pdf) I have seen that they mention a "minimal treshold reads per kilobases per millon mapped reads (RPKM) > 0.1". Does this mean that in order to say that a tissue is expressed needs to have at least 0.1 RPKM?

ADD REPLYlink written 4 months ago by GabrielMontenegro330
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