Question: Multiple tissue eQTL list
2
gravatar for Randel
6.2 years ago by
Randel40
United States
Randel40 wrote:

I know there is a similar question asked 3.7 years ago: Eqtl Database Available?. I'd like to see if there is any recent multiple tissue eQTL list available. Thanks!

 

Here is a list of resources I am aware of:

NCBI eQTL Browser: there is only one study using RNA-seq, which is only one tissue.

eQTL browser @ the Pritchard lab: last updated in June 2012.

Genevar: the latest study for eQTL is in 2012.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Randel40
1

Genenetwork.org hosts multiple eQTL datasets for different mouse tissues and a few human tissues.

ADD REPLYlink written 6.2 years ago by Ashutosh Pandey12k

Thanks! I will take a look at it.

ADD REPLYlink written 6.2 years ago by Randel40
2
gravatar for J.F.Jiang
6.2 years ago by
J.F.Jiang860
China
J.F.Jiang860 wrote:

actually, multiple groups are heading forward to study the eQTLs across tissues, such as GTex and TCGA.

However, none of these studies is open for public, which might be done after the paper is published.

So, just wait.

ADD COMMENTlink written 6.2 years ago by J.F.Jiang860

Thanks for your answer! I think we can download some eQTLs on the GTEx portal now. But for TCGA, there seems no eQTL list available, but we may download the raw data and calculate eQTLs by ourselves.

ADD REPLYlink written 6.2 years ago by Randel40
1

RIGHT, for gtex, if you can access the data, such as dbGaP, you can certainly obtain the eQTLs, however, I still consider they are not avaiable, at least you can not use these data for publicaition now.

For tcga, if the data has already been accessful, e.g., the corresponding paper has been published, you can use the genotype data and the expression, e.g. microarray, and RNASeq data, to fetch the eQTLs. But be carefully, those eQTLs are cancer-related other than common ones, which means these data might not be applied to annotate the common SNPs.

ADD REPLYlink written 6.2 years ago by J.F.Jiang860
1

For GTEx, if you log in and click on datasets you can access the eQTL data. They have released files containing all significant eQTLs for the Pilot release.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by komal.rathi3.7k

For GTEx, you can at least search or download eQTL results here. Thanks for your remind about TCGA!

 

ADD REPLYlink written 6.2 years ago by Randel40

Yes, though the sample size is variously different. It provides available eQTLs across tissues.

Let's wait the release of TCGA, or we can get the SNPs data from dbGap, then ...

ADD REPLYlink written 6.2 years ago by J.F.Jiang860
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