Regulatory feature to gene annotation

Question

[aponce]

Hi, I have a list of thousands regulatory features from the Ensembl Regulatory Build and I want to associate each one to a gene or transcript from the ensembl gene annotation. I looked in the "feature context" in ensembl web page and I could see the ensembl gene associated to a specific regulatory feature, e.g. ENSR00000297462 to ENSG00000057704, I want to do this but in a much larger scale. I've searched a lot here in Biostars and in the ensembl help web page and I can't find any solution. The annotation has CTCF bindings, open chromatin sites and enhancers so I think in these cases that's not possible but for promoters (proximal promoters) it can be done.

GeneCards has an annotation for enhancers called Genehancer which match a group of genes with a enhancer location, I downloaded the data but they have its own IDs and I don't know how to translate those into ensembl ENSR IDs. I hope if this is possible. Thank you very much for your help.

Answer 1

[Emily]

We do not have linking between regulatory features and genes in Ensembl. The feature context does not tell you which genes are associated with the regulatory feature, just which ones are near to it. If you are happy to find out which genes are near to your regulatory features, you could look at using the Perl API or BioMart to get the locations of the regulatory features and identify genes, say, 5kb either side.

Answer 2

[GouthamAtla]

You can search literature that predicts the enhancer-promoter interactions.For example, you may find papers like Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin