Hello!
I’ve a silly question concerning the way of calculating the distance between genes on the same chromosome but on different strand. I’ve retrieved the genes position from Ensembl. For example I’ve would like to calculate the distance between:
- GAS6 Start-113820549 End-113864076 reverse strand
- MCF2L Start-112877718 End-113103082 forward strand
I’ve read several post on Biostars about it and I’m completely lost because of the diverging opinions. One of the solution given in this post was the formula:
max(start_gene1, start_gene2) - min(end_gene1,end_gene2).
If I apply this formula (113820549-113103082) the distance between the genes GAS6 and MCF2L equals to 717467nt. Is it correct to assume that?
Thanks you for your attention and responses!
1 answer
To me, distance between two genes would be the distance between the two transcriptional start sites. So I would just take the two TSS and get the absolute differences between them. This makes sense if you are looking into transcriptional regulation as its about promoters ( even if its about enhancers, they usually loop to the gene promoters).
If you are looking for something else, I am not sure what would be the best to consider as distance in your case.
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Yes, that is correct - even you can cross-check using
closestBedfrom bedtools. Please see the answer of @Singh in this post (Distance between two gene sets)