MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants

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dc.contributor.authorJin, Weijia
dc.contributor.authorXia, Yi
dc.contributor.authorNizomov, Javlon
dc.contributor.authorLiu, Yunlong
dc.contributor.authorLi, Zhigang
dc.contributor.authorLu, Qing
dc.contributor.authorChen, Li
dc.contributor.departmentMedical and Molecular Genetics, School of Medicine
dc.date.accessioned2024-11-12T10:40:23Z
dc.date.available2024-11-12T10:40:23Z
dc.date.issued2024
dc.description.abstractSummary: Massively parallel reporter assay (MPRA) is an important technology for evaluating the impact of genetic variants on gene regulation. Here, we present MPRAVarDB, an online database and web server for exploring regulatory effects of genetic variants. MPRAVarDB harbors 18 MPRA experiments designed to assess the regulatory effects of genetic variants associated with GWAS loci, eQTLs, and genomic features, totaling 242 818 variants tested more than 30 cell lines and 30 human diseases or traits. MPRAVarDB enables users to query MPRA variants by genomic region, disease and cell line, or any combination of these parameters. Notably, MPRAVarDB offers a suite of pretrained machine-learning models tailored to the specific disease and cell line, facilitating the prediction of regulatory variants. The user-friendly interface allows users to receive query and prediction results with just a few clicks. Availability and implementation: https://mpravardb.rc.ufl.edu.
dc.eprint.versionFinal published version
dc.identifier.citationJin W, Xia Y, Nizomov J, et al. MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants. Bioinformatics. 2024;40(10):btae578. doi:10.1093/bioinformatics/btae578
dc.identifier.urihttps://hdl.handle.net/1805/44496
dc.language.isoen_US
dc.publisherOxford University Press
dc.relation.isversionof10.1093/bioinformatics/btae578
dc.relation.journalBioinformatics
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.sourcePMC
dc.subjectGenetic variation
dc.subjectGenome-wide association study
dc.subjectMachine learning
dc.subjectQuantitative trait loci
dc.titleMPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants
dc.typeArticle
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