GTEX - how to upload more than one rsIDs to get gene expression or eQTL information

Question

[SGMS]

Hi everyone,

I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically.

I looked on GTEx but I only found the option of using one SNP at a time or put a list of SNPs but that is with additional info I don't have.

Does anyone know how to upload multiple rsIDs on GTEx?

Thanks a lot

[optimistsso4co3]

Did you figure it out?

Answer 1

[optimistsso4co3]

Did you figure it out?

[SGMS]

Hello,

I downloaded the latest GTEx version which included SNPs and found common SNPs of GTEx with my dataset. I then compared the effect sizes (direction of betas) of my dataset to the ones in GTEx.

Hope that helps!

[zhuyuex96]

I want to Know how to get the GTEx data? Thanks for your help

[SGMS]

Hi, sure!

You can download anything you need from https://www.gtexportal.org/home/datasets.

I wanted version 7 (v7) which has to do with the assembly hg19 but there's a newer version for hg18 as well. I specifically downloaded the GTEx_Analysis_v7.metasoft.txt.gz from: "Multi-tissue eQTL data" and GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLI.

Hope this helps!

[IZT]

Hello, I am a still a student, so a beginner in this field, but I would need help regarding GTEX and how to work with it. I was given a task, which includes finding and extracting eQTLs for specific genes from the GTEX portal and then linking those eQTLs to the expression of those genes: increased, reduced or neutral with regard to it. Unfortunately, I had no instructions on how to do it and I was wondering whether someone could help me out on both by briefly outlining the process. That would be of great help! Thank you so much in advance!

[SGMS]

Hi Ivet,

The good news is that your task is pretty simple if you're not looking for hundreds of genes. You need to go to: https://gtexportal.org/home/ and search for the gene of your interest. Then, on the left hand side, GTEx shows you the "Single-tissue eQTLs" which you can download as a .csv file. As you will see, there will be a gene symbol, a p-value and the tissue -amongst others-. When you see your gene of interest, it means that it is expressed in the tissue reported next to it. From the p-value, you will understand how significant this expression is.

[IZT]

Hi, and would it be possible to link the extracted data to the gender, associated medical conditions etc of the patient? Or directly to download the data of the eQTLs with this information in a single table?

[SGMS]

Hi,

Unfortunately, this is not possible using the database itself. I haven't downloaded the latest version of the full data per tissue but I don't think it has this kind of information.

You could always send an email to the GTEx helpdesk team and ask them just to be sure!

Also, if you think this thread helped you, press the like button on the question at the top so other people know they can find relevant GTEx info :)