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

Bioinformatics (Oxford, England) Pub Date : 2024-10-01 DOI:10.1093/bioinformatics/btae578

Weijia Jin, Yi Xia, Javlon Nizomov, Yunlong Liu, Zhigang Li, Qing Lu, Li Chen

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Abstract

Summary: 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.

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MPRAVarDB：用于探索基因变异调控效应的在线数据库和网络服务器。

摘要：大规模并行报告分析（MPRA）是评估基因变异对基因调控影响的一项重要技术。在此，我们介绍一个用于探索基因变异调控效应的在线数据库和网络服务器 MPRAVarDB。MPRAVarDB 包含 18 个 MPRA 实验，旨在评估与 GWAS 基因座、eQTL 和基因组特征相关的遗传变异的调控效应，共测试了 30 多种细胞系和 30 多种人类疾病或性状的 242,818 个变异。MPRAVarDB 使用户能够按基因组区域、疾病和细胞系或这些参数的任意组合查询 MPRA 变异。值得注意的是，MPRAVarDB 提供了一套针对特定疾病和细胞系的预训练机器学习模型，便于预测调控变异。用户友好的界面让用户只需点击几下就能收到查询和预测结果。可用性：https://mpravardb.rc.ufl.edu.Supplementary 信息：补充数据可在 Bioinformatics online 上获取。

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Bioinformatics (Oxford, England)

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