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How does GOntact work?

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). GO categories are "transmitted" to noncoding elements from the genes that they are in contact with. 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 (e.g. elements that are specifically active in a given biological condition) with the frequency of elements associated with the same GO category in a background set (e.g. CREs detected in a broader set of biological conditions). If no background set is provided, the expected GO frequencies are computed based on the entire genome.

Checkout this page for the source code, a detailed documentation and usage examples for the standalone GOntact version.

Datasets used in the GOntact webserver (version 1.0)

Genome annotations

Genome annotations were downloaded from the Ensembl database, release 115 for human and release 102 for mouse. They correspond to the hg38 and mm10 genome assemblies. These coordinates are used to determine regulatory domains and to annotate baited restriction fragments for the GOntact approach.

Gene Ontology annotations

Gene Ontology annotations were downloaded from http://geneontology.org. They correspond to the release 2025-10-10 of the Gene Ontology database. We used the Mouse Genome Informatics (MGI) annotations for mouse and the EBI Gene Ontology Annotation Database for human. We used the "basic" version of the GO database (go-basic.obo) to analyze the hierachical structure of GO annotations and to propagate GO annotations upstream in the graph.

Promoter Capture Hi-C data

The data used here were taken from the publication by Laverré et al., Genome Research, 2022. The raw PCHi-C data was combined from multiple sources, listed below. The data was processed with a pipeline based on HiCUP and CHiCAGO.

species identifier tissue/cell type data source
human NB naïve B lymphocytes Javierre et al., 2016
human TB total B lymphocytes Javierre et al., 2016
human cardio cardiomyocytes Choy et al., 2018
human hESC embryonic stem cells Freire-Pritchett et al., 2017
human EP endothelial precursors Javierre et al., 2016
human Ery erythroblasts Javierre et al., 2016
human FoeT fetal thymus Javierre et al., 2016
human CD34 CD34+ lymphocytes, hematopoietic progenitors, ex vivo Mifsud et al., 2015
human PEK_early differentiated primary epidermal keratinocytes Rubin et al., 2017
human PEK_late differentiated primary epidermal keratinocytes Rubin et al., 2017
human PEK_undiff primary epidermal keratinocytes Rubin et al., 2017
human Bcell B lymphocytes, EBV-transformed Mifsud et al., 2015
human Mac0 macrophages M0 Javierre et al., 2016
human Mac1 macrophages M1 Javierre et al., 2016
human Mac2 macrophages M2 Javierre et al., 2016
human MK megakaryocytes Javierre et al., 2016
human Mon monocytes Javierre et al., 2016
human hNEC neuroepithelial cells Freire-Pritchett et al., 2017
human Neu neutrophils Javierre et al., 2016
human pre_adipo primary white preadipocytes Pan et al., 2018
human NCD4 naive CD4 T lymphocytes Javierre et al., 2016
human NCD8 naive CD8 T lymphocytes Javierre et al., 2016
human TCD4Act activated total CD4 T lymphocytes Javierre et al., 2016
human TCD4MF total CD4 T lymphocytes Javierre et al., 2016
human TCD4Non non-activated total CD4 T lymphocytes Javierre et al., 2016
human TCD8 total CD8 T lymphocytes Javierre et al., 2016
mouse preB_aged pre-B cells Koohy et al., 2018
mouse preB_young pre-B cells Koohy et al., 2018
mouse ESC embryonic stem cells Schoenfelder et al., 2015
mouse ESC_18 embryonic stem cells Schoenfelder et al., 2018
mouse ESC_wild embryonic stem cells Novo et al., 2018
mouse ESC_NKO embryonic stem cells, Nanog deficient Novo et al., 2018
mouse EpiSC epiblast stem cells Novo et al., 2018
mouse ESd_starved ES-derived multipotent hematopoietic progenitor cells Comoglio et al., 2018
mouse ESd_TPO ES-derived multipotent hematopoietic progenitor cells Comoglio et al., 2018
mouse FLC fetal liver cells Schoenfelder et al., 2015
mouse preadip_4H pre-adipocytes Siersback et al., 2017
mouse preadip_D0 pre-adipocytes Siersback et al., 2017
mouse preadip_D2 pre-adipocytes Siersback et al., 2017
mouse TSC trophoblast stem cells Schoenfelder et al., 2018