Gene Ontology enrichments based on chromatin contacts for cis-regulatory elements

GOntact evaluates Gene Ontology (GO) enrichments for sets of cis-regulatory elements (CREs). To associate CREs to genes, GOntact uses chromatin contacts obtained from chromosome conformation capture data (Hi-C, promoter capture Hi-C, micro-C etc). Here we use PCHi-C chromatin contacts compiled by Laverré et al., Genome Research, 2022 (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. Click here to download an example dataset, containing genome annotations, CRE coordinates and PCHi-C data.

To perform GO enrichment analyses by associating CREs to genes based on genomic proximity, you can use GREAT. To run our implementation of GREAT using the same genome annotations and Gene Ontology data used in GOntact, you can do so here.

1. Select the Gene Ontology domain for which you want to compute an enrichment

biological process
molecular function
cellular component

2. Select a dataset

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

GOntact computes GO enrichments by comparing a foreground set of CREs (e.g. those specifically active in a given biological condition) with a background set of CREs (e.g. CREs detected in a broader set of biological conditions). They have to be provided in bed format, with at least 3 tab-separated fields (chromosome, start position, end position). Input the coordinates of the foreground regions (bed format):

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

If no background set of CREs is provided, GOntact will compute background GO frequencies based on the whole genome.

3. Selection of chromatin contacts

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):