Question: Data set with both genetic variants and gene expressions
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gravatar for cindy.perscheid
6 days ago by
Hasso Plattner Institute, Potsdam, Germany
cindy.perscheid30 wrote:

Hi there,

as it seems getting access to the recently published GTEx data set (https://www.biorxiv.org/content/biorxiv/early/2016/09/09/074443.full.pdf; see discussion here https://www.biostars.org/p/283484/#283521) is quite hard for non-US institutions, I was wondering whether it is easier to just use another data set for my purpose.

Do you know of any data set that contains both genetic variants (coding and/or non-coding) and gene expression data? I want to develop an algorithm to derive causal relationships between a variant and the gene expressions. The GTEx data set seemed to be exactly what I needed. Is there anything similar available, e.g. for cancer? I know I can download both genetic variants and gene expressions from GDC, but these would probably have to undergo a lot of preprocessing, e.g. to select only a couple of genetic variants (which is beyond my biological expertise) or select only gene expression outliers as done in the GTEx data set.

Any suggestions are highly appreciated!

Best,

Cindy

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