Gene Ontology enrichments based on chromatin contacts for noncoding elements

GOntact aims to evaluate Gene Ontology (GO) enrichments for sets of noncoding elements. To do this, GOntact uses chromatin contacts determined with the promoter capture Hi-C (PCHi-C) approach. GO categories are "transmitted" to noncoding elements from the genes that they are contacted by in the PCHi-C data. The statistical significance of GO enrichments is evaluated with binomial tests, which compare the frequency of elements associated with a given GO category in a foreground set with the frequency of elements associated with the same GO category in a background set. By default, the coordinates of enhancer elements predicted by ENCODE are used as a background set. For the GOntact webserver, PCHi-C chromatin contacts are those compiled by Laverre et al., Genome Research, 2022. The data used in this version of the GOntact webserver are described here. If you want to run GOntact on a different organism or a different set of PCHi-C samples, please see our command-line version on GitLab. If you want to run GREAT using the same genome annotations and Gene Ontology data, you can do so here.

Select the Gene Ontology domain for which you want to compute an enrichment:
biological process
molecular function
cellular component

Select the genome you want to analyze:
human (hg38)
mouse (mm10)

Input the coordinates of the foreground regions (bed format):

(Optional) Input the coordinates of a custom set of background regions (bed format):

Selection of chromatin interactions:

Minimum number of PCHi-C samples:
Minimum CHiCAGO score:
Minimum distance between contacted regions (bp):
Maximum distance between contacted regions (bp):
Maximum distance between elements and contacted fragments (bp):
Size of the basal regulatory domain to be included (bp):