Question: How to integrate GTEx data for variant annotation to understand the tissue specific expression?
1
gravatar for bioinfo89
11 weeks ago by
bioinfo8940
bioinfo8940 wrote:

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!

snp next-gen • 194 views
ADD COMMENTlink modified 11 weeks ago by EagleEye5.7k • written 11 weeks ago by bioinfo8940

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 written 17 days ago by SGMS40
1

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 written 10 days ago by bioinfo8940

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 written 10 days ago by SGMS40

Yes, correct. Thats exactly what I did.

ADD REPLYlink written 9 days ago by bioinfo8940

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

ADD REPLYlink written 9 days ago by SGMS40
0
gravatar for EagleEye
11 weeks ago by
EagleEye5.7k
Sweden
EagleEye5.7k wrote:

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

ADD COMMENTlink written 11 weeks ago by EagleEye5.7k

Thanks EagleEye for the articles I will check them.

ADD REPLYlink written 11 weeks ago by bioinfo8940
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