Entering edit mode
5.4 years ago
Hann
▴
110
Hello all,
I've detected selection using different methods. let's talk about CLR method.
What I did is I selected positions that have 1% highest CLR value (high CLR values denote a candidate region for a selective sweep). and crossed the position with the annotation and I got 1200 genes.
Imagine that MYB transcription factor was in the list of candidate regions that are under selection.
There is probably several hundreds of MYB in the genome, so it's very likely that I can find them in the peaks by chance.
How would you really say this gene was under selection if it's at the end is a matter of chance?
What do you mean?
What I meant is that you can't find a single gene under selection. because as I said for example MYB gene was found in the peak (meaning that it's under selection), but MYB gene is also present somewhere else in the genome. So MYB gene might be present in the peak just by chance
MYB has many binding sites across the genome, as you implied. Assuming that you have identified the peaks correctly and have set your thresholds, then the peak may be valid. However, cellular activity / transcription of downstream target genes may only occur at certain MYB-binding sites where other factors permit this.
Have you considered overlaying your peaks with other information relevant to transcription, such as acetylation marks of enhancers (H3K27ac)? You could also try to gauge the conservation of the region via, e.g., phyloP scores. I think that there are many ways to address the question that you are posing, and the more ideas, the better. I will ask some colleagues.