How to retrieve enhancer regulated genes

Question

[b8921019]

Hi,

I am trying to identify super enhancer-regulated genes. I used "SEdb" to find the super enhancers in my cell line and try to upload the bed file to locate its associated genes. However, the website didn't respond to my input. I think my bed file is correct, but I cannot get my data analyzed. Does anyone know how to use this website? Are there other methods to extract the genes regulated my enhancers?

Thanks

Answer 1

[gdeniz]

Enhancer - target gene relationships are cell type specific. A popular strategy without availability of 3D chromatin contact data is to look for the nearest (expressed) gene (which is ~40-60% accurate based on recent publications). If you have a bed file of enhancers you can find the nearest gene using annotatePeaks.pl function from the Homer suite. Alternatively, you could get a bed file of transcriptional start sites (TSS) for your organism (potentially filter for expressed genes based on RNA-seq data of your cell type) and then use bedtools closest (bedtools suite) to determine the nearest TSS.