Entering edit mode
5 months ago
goyal.shiwali
▴
20
Hello,
I am working on the mouse lens, in which I have obtained lens fiber and epithelium at two-time points, E17 (embryonic day 17) and P2 (postnatal day 2) for two different mouse strains, C57BL/6j and FvBN. I have a list of differentially expressed genes from the RNA sequencing. I aim to discover why the genes are differentially expressed between the epithelium and fibers within the same or between two different mouse strains. Now I need to know the reasons for differential gene expression.
I am not sure how to proceed further. If you have any suggestions, that would be really helpful to me
Thanks
Should you not be approaching this with a hypothesis on what you expect to happen instead of looking at what's different first and wondering why? Anyway, try GSEA-like approaches to see if the genes being differentially expressed and enriched for some biological pathway etc.
Hello, Thanks for the response I am not interested in looking for biological pathways. I want to stay focused on why genes are expressed differently in different mouse types. I may be wrong, but I am wondering if any eQTL or transcription factor binding might be the reason behind that.
OK, so you want to figure out the mechanism behind allele-specific differential expression. You're probably underpowered for an eQTL-type analysis. For other things like transcription factor binding or chromatin accessibility, you'll need more than just RNAseq data.
It's a bit difficult to do because any number of things could cause the patterns of differential gene expression that you observe. It could be something cis-acting, something trans-acting, both, etc. I don't really think your RNAseq data alone can give answers like "this genetic variant is responsible for the time point differential gene expression in c57 vs. fvb mice".
Hello dshull thanks for the response
I was wondering if there is any eQTL database for mouse, and I can use that to look for the eQtls which might be affecting the expression pattern. I already have the Genome data for both the mice strains (C57 and FvBN) from NCBI