Eqtl Database Available?

Question

[Krisr]

Hi All,

I am interested in identifying if any of a few hundred SNPs have eQTL data. Other than mining the literature, does anyone know of any databases or repositories of such data, that I can query?

Thanks!

K

[User 7754]

Hi,

From your answers it seems as the databases available for now on eQTL are: eQTL resources and browser @ the pritchard lab (uchicago)/ GTEx (Genotype-Tissue Expression) eQTL Browser (ncbi)/ Genevar (GENe Expression VARiation)/ SCAN

Is anybody aware of any other?

Thank you, -f

Answer 1

[Larry_Parnell]

I only have data from the following rather early larger-scale eQTL papers and the occasional eQTL information from GWAS papers pertinent to our research.

Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KC, Taylor J, Burnett E, Gut I, Farrall M, Lathrop GM, Abecasis GR, Cookson WO. (2007) A genome-wide association study of global gene expression. Nat Genet. 2007 Oct;39(10):1202-7.

Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet. 2007 Feb;39(2):226-31.

eQTL data from Stranger, Dermitzakis first paper (2007) using HapMap cell lines

Zhang W, Duan S, Kistner EO, Bleibel WK, Huang RS, Clark TA, Chen TX, Schweitzer AC, Blume JE, Cox NJ, Dolan ME. (2007) Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet. 2008 Mar;82(3):631-40.

As looking for, downloading and maintaining these data are a bit painful and certainly time-consuming, I, too, would be interested in a central repository.

Answer 2

[Bert Overduin]

The Sanger eQTL data mentioned by Larry are available as a DAS source.

[Larry_Parnell]

Rig, thanks for the reminder.

[Larry_Parnell]

Right, thanks for the reminder.

Answer 3

[Argossy]

seeQTL: A searchable database for human eQTLs

http://www.bios.unc.edu/research/genomic_software/seeQTL/

http://bioinformatics.oxfordjournals.org/content/early/2011/12/13/bioinformatics.btr678.abstract?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=seeqtl&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT

Answer 4

[Rossella]

SCAN contains eQTL information for some of the most common populations. You can query it at: http://scan.bsd.uchicago.edu/newinterface/index.html

Answer 5

[Casey Bergman]

You can use the GeneVar Java webstart tool to paste or load a list of SNPs (i.e. rs13277113) to find SNP-gene expression associations around your SNPs of interest (e.g. cis-eQTLs). The system currently includes two studies from the Dermitzakis lab, but can be extended to load user data for expression (Illumina arrays) and genotypes.

EDIT:

You can also try the eQTL browser from the Pritchard Lab, which is a gbrowser containing results compiled from these publications:

• Myers et al. (2007)
• Stranger et al. (2007)
• Schadt et. al (2008)
• Veyrieras et al. (2008)
• Pickrell et al. (2010)
• Montgomery et al. (2010)
• Zeller et al. (2010)

Answer 6

[Khader Shameer]

I just heard of this new initiative from NCBI: GTEx (Genotype-Tissue Expression) eQTL Browser.

I think this resource is relatively new and an exclusive manuscript is not yet available, but there is a distinct mention about GTEx in this review article. Also there is a detailed tutorial to get you started.

[Larry_Parnell]

I have taken this one for a spin and like it. It is limited, for now, to 7 cell types/lines. Hopefully more are added. Nice attribute to have links to GWAS - but painful to select all those that pertain to our interest of obesity & blood lipids.

Answer 7

[Andrew Johnson]

There are many more eQTL sources published. I've compiled a catalog of available results (not currently public). Feel free to contact me if you want more information: Andrew - adjbiotech ObviousInBetweenSymbol ObviousHotmailDomainEnding

[J.F.Jiang]

could you kindly offer me this catalog or some suggestion of eqtl sources? if you can email to me [e-mail] or you email?

[Krisr]

I'd also be interested in this.. I've sent an email to the address posted, Thanks!