Breeze, Charles E;
Haugen, Eric;
Gutierrez-Arcelus, María;
Yao, Xiaozheng;
Teschendorff, Andrew;
Beck, Stephan;
Dunham, Ian;
... Berndt, Sonja I; + view all
(2024)
FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases.
Genome Biology
, 25
(1)
, Article 3. 10.1186/s13059-023-03126-1.
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Abstract
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.
| Type: | Article |
|---|---|
| Title: | FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1186/s13059-023-03126-1 |
| Publisher version: | http://dx.doi.org/10.1186/s13059-023-03126-1 |
| Language: | English |
| Additional information: | © 2024 BioMed Central Ltd. This article is licensed under a Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Gene regulation, Functional annotation, Variant scoring, Regulatory elements, Genome-wide association study (GWAS), Expression quantitative trait locus (eQTL), Massively parallel reporter assay (MPRA), Activity-by-contact (ABC), DNase-seq, Transcription factor (TF), CRISPR (clustered regularly interspaced short palindromic repeats), Single guide RNA (sgRNA) |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10185342 |
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