This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tissue Specific Gene-Gene Similarity (Co-Expression)

Hi,

I am looking for a good way to compute similarity between pairs of genes for brain tissue. The purpose is to post-analyse GWAS data for the Alzheimer's disease. This is what I am currently thinking:

-- I "think" the best way is to find tissue specific eQTL SNPs for each genes which I guess I can find it from here (http://www.regulomedb.org/ ) and compute gene-gene similarity using gene-expression data. But I don't where to get this one. Is there any standard tissue specific eQTL for SNP ? Is there any standard gene co-expression matrix that I can download?

-- I tried to do that with GO terms but first of there are not tissue specific. Plus computing all Gene-Gen similarities are computationally very expensive. (BTW can I find it pre-computed somewhere?) Plus, mapping from SNPs to gene is just based on proximity (LD) which I guess too noisy for my application.

Any idea, suggestion?

Thanks

gene expression similarity clustering
• 3,238 views • link
updated by Charles Warden Charles Warden • written by GenomicEnthusiast • GenomicEnthusiast

1 answer

It is a somewhat indirect strategy, but you can use TiGER to identify genes with tissue-specific expression. If your gene of interest is tissue-specific, you can download a table for all tissue-specific genes for that organ:

http://bioinfo.wilmer.jhu.edu/tiger/

• 0 views • link
written by Charles Warden Charles Warden

Log in to answer this question.

More posts like this