Link Genomic Regions to Target Genes

Just want to find the target genes for your genomic regions? Upload your set of genomic regions to assign them to target genes based on the selection of regulatory regions, including enhancers, promoters, whole genome, exons, introns, etc. For enhancer to target gene assignments, we use human genome version hg19, however, multiple species and multiple reference genome versions are available for all other regulatory regions. The human enhancer to target gene assignments can be generated by selecting data from a variety of sources and methods.


Analysis

Step 1: Upload the file

Select Species and genome version

Currently, ‘smart’ enhancer-target gene links are only available for hg19. All other genomes link to the gene with the nearest TSS. ‘Smart’ enhancer-target links will be available for hg38 soon.
Note: the input bed file is assumed to be 1-based

Input file :

The following formats are fully supported via their file extensions: .bed, .broadPeak, .narrowPeak, .gff3, .gff2, .gff, and .bedGraph or .bdg. BED3 through BED6 files are supported under the .bed extension. Files without these extensions are supported under the conditions that the first 3 columns correspond to 'chr', 'start', and 'end' and that there is either no header column, or it is commented out. Example file can be found here

Step 2: Assign peaks in


Note: To annotate the entire genome with enhancer-gene target links, combine the Promoters 5kb option with one of the All distal regions (using enhancer-gene target links) options. Some choices may have one option.

Step 3: Choose how to assign to:

Complete

You have successfully completed all steps.