Multiple tissue eQTL list

Question

[Randel]

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.

[Ashutosh Pandey]

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

[Randel]

Thanks! I will take a look at it.

Answer 1

[J.F.Jiang]

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.

[Randel]

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.

[J.F.Jiang]

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.

[komal.rathi]

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.

[Randel]

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

[J.F.Jiang]

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 ...