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Question: How to integrate GTEx data for variant annotation to understand the tissue specific expression?
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Hi All,

I have a list of variants and I want to integrate the data from GTex database. Is there any specific way to do this? The files provided on the GTEx portal are quite complicated to understand.

I want to extract the information related to variant and its expression in all the tissues. (eg. if a variant is rsxxxxxxx, so how it affects the gene expression tissue wise is what I want to add in my study)

I downloaded the file GTEx_Analysis_v7_eQTL.tar.gz from the portal but it has rsIDs and p-value for all the tissue types. I am not sure how to use this data to make sense and integrate with the SNP list I have.

Another thing to mention is that, DBNSFP database integrated in annovar also provides 2 columns that is GTEx gene and tissue but there is no clarification on what exactly it is trying to display in those columns.

Any help of suggestions will be appreciated.

Thanks!

ADD COMMENTlink 18 months ago bioinfo89 • 40 • updated 18 months ago EagleEye 6.4k
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Hi bioinfo89,

Did you manage to find a solution? I keep looking for the exact same things but cannot find any help.

Thanks a lot!

ADD REPLYlink 16 months ago
SGMS
• 60
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Hi SGMS,

Yes, I downloaded the metasoft file from the GTEx portal (https://storage.googleapis.com/gtex_analysis_v7/multi_tissue_eqtl_data/GTEx_Analysis_v7.metasoft.txt.gz) and corresponding rsid lookup file (https://storage.googleapis.com/gtex_analysis_v7/reference/GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLINKQC.lookup_table.txt.gz). Integrated the information and used p-value < 0.05 as cutoff to see which tissue expression does the SNP affect.

Hope that helps!

ADD REPLYlink 16 months ago
bioinfo89
• 40
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Hi bioinfo89,

Thank you very much for your reply. Just to make sure I got it right; I downloaded the files. The rsID look-up file has variant_id and rsID columns. So when you say "Integrated the information", you mean that you matched your rsIDs of interest with the variant_ID so you could find that variant_ID in the metasoft file and therefore find which tissue the SNP affects. Is that right?

Thanks a lot once again

ADD REPLYlink 16 months ago
SGMS
• 60
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Yes, correct. Thats exactly what I did.

ADD REPLYlink 16 months ago
bioinfo89
• 40
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Brilliant, thanks so much! This is of such a great help!

ADD REPLYlink 16 months ago
SGMS
• 60

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