Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States.
Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
Bioinformatics. 2024 Oct 1;40(10). doi: 10.1093/bioinformatics/btae578.
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.
大规模平行报告分析（MPRA）是评估遗传变异对基因调控影响的重要技术。本文介绍了 MPRAVarDB，这是一个在线数据库和网络服务器，用于探索遗传变异的调控效应。MPRAVarDB 包含 18 个 MPRA 实验，旨在评估与 GWAS 位点、eQTL 和基因组特征相关的遗传变异的调控效应，共测试了超过 30 种细胞系和 30 个人类疾病或特征的 242818 个变体。MPRAVarDB 允许用户按基因组区域、疾病和细胞系，或这些参数的任意组合查询 MPRA 变体。值得注意的是，MPRAVarDB 提供了一套针对特定疾病和细胞系量身定制的预训练机器学习模型，有助于预测调控变体。用户友好的界面允许用户只需点击几下即可接收查询和预测结果。
