I have genomic coordinates in a .bed file and I want to see which regions contain enhancer elements.
What is the best way to go about this?
I have found the enhancer atlas 2.0, which looks pretty helpful:
This has the benefit of being cell-type specific. But it is annotated to hg19 and my data is aligned to and annotated with genes from GRCh38. I imagine I could lift over the coordinates without too much difficulty...
I've also found the GeneHancer from UCSC which could be helpful.
It's difficult to know exactly how to start as I don't know much about the world of regulatory elements and it seems like a bit of a minefield with regards to what is considered an enhancer or not.
1 answer
Even if you do manage to annotate the enhancer elements to your bed file, I'm not sure it will be useful.for 2 reasons:
1) You have no way of knowing if any enhancer element was active in your data. 2) While the proximity of an enhancerA to gene1 is a reasonable predictor of the the probability of enhancerA acting on gene1, it is by no means reliable to state that "gene1 was expressed due to activity of enhancerA which is the closest enhancer".
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