Closed:Want to get advice on some trans-eQTL result

Question

[namkungho87]

Hi,

I am performing both cis and trans eQTL for two genes of interest (we have profiled two specific genes of interest using qRT-PCR). Anyway, using Matrix-eQTL tool, I have tried to find both cis and trans eQTLs. Interestingly, whereas there are NO significant eQTL for both genes, there were many trans-eQTLs of significance (FDR). I tried to look into the detailed distribution of gene expression, and realized the distribution is like the attached picture:

https://drive.google.com/file/d/1kslgqOpLG8-VznBE2SmmtS3gLTseBnJB/preview

Given that there were only two subjects (among 94 subjects) that have ALT/ALT, I am wondering if the result from this analysis is still valid or not..

Please advise me.

Thanks!