Download eQTL data of one specific gene for all tissues from GTEx

Question

[Jeol]

Hi, can you help me with this:

I have a gene of interest, i.e, AhR. I want to download its eQTL data for all tissues from GTEx.

I find I cannot do it from GTEx Portal: https://www.gtexportal.org/home/datasets.

I guess it is requried with using R code with GTEx APIs: https://gtexportal.org/home/apiPage

Am I right, can anyone help me kindly with it, many thanks!

Answer 1

[bk11]

Please kindly check your result here. You can click csv and download the date in this link.

OR

If you prefer to use R, there is apackage called xQTLbiolinks, please play with it. It should help you get the data from GTEx.

library(xQTLbiolinks)
library(data.table)
library(stringr)
eqtlMeta <- xQTLquery_eqtl(gene="AHR")

head(eqtlMeta)
Key: <variantId>
               variantId     snpId          gencodeId geneSymbol                    tissueSiteDetail    pValue        nes        se mValue datasetId
                  <char>    <char>             <char>     <char>                              <char>     <num>      <num>     <num>  <num>    <char>
1: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR                             Thyroid 0.2182800  0.0503958 0.0408840  0.390   gtex_v8
2: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR                              Testis 0.3610070  0.0382198 0.0417694  0.367   gtex_v8
3: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR    Small Intestine - Terminal Ileum 0.7702310 -0.0158787 0.0542557  0.229   gtex_v8
4: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR        Brain - Frontal Cortex (BA9) 0.8535050 -0.0150914 0.0815739  0.343   gtex_v8
5: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR Skin - Not Sun Exposed (Suprapubic) 0.0861401  0.0746005 0.0433745  0.553   gtex_v8
6: chr7_16637245_C_G_b38 rs4719473 ENSG00000106546.12        AHR                              Vagina 0.2760140 -0.1388670 0.1268800  0.300   gtex_v8