How to integrate GTEx data for variant annotation to understand the tissue specific expression?

Question

[bioinfo89]

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!

[SGMS]

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!

[bioinfo89]

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!

[SGMS]

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

[bioinfo89]

Yes, correct. Thats exactly what I did.

[SGMS]

Brilliant, thanks so much! This is of such a great help!

Answer 1

[EagleEye]

These articles will give you some idea to proceed with your analysis.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues

Genetic effects on gene expression across human tissues

Mapping eQTLs in the Norfolk Island Genetic Isolate Identifies Candidate Genes for CVD Risk Traits

[bioinfo89]

Thanks EagleEye for the articles I will check them.