MPRAbase a Massively Parallel Reporter Assay database

IF 6.2 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Genome research Pub Date : 2025-04-22 DOI:10.1101/gr.280387.124

Jingjing Zhao, Fotis A Baltoumas, Maxwell A Konnaris, Ioannis Mouratidis, Zhe Liu, Jasmine Sims, Vikram Agarwal, Georgios A Pavlopoulos, Ilias Georgakopoulos-Soares, Nadav Ahituv

引用次数: 0

Abstract

Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of these experiments. To address this, we developed MPRAbase, a manually curated database that currently harbors 130 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface serves as a centralized user-friendly repository to examine online the activity of regulatory elements across cell types and organisms, and to download MPRA data for independent analysis.

查看原文本刊更多论文

MPRAbase：大规模并行报告分析数据库

大规模平行报告基因分析（MPRAs）代表了一套高通量技术，可以测量数千个序列/变异对基因调控活性的功能影响。MPRA技术有几种不同的变体，它们被用于许多应用，包括调控元件的发现、变异效应测量、饱和诱变、合成调控元件的生成或进化基因调控差异的表征。尽管它们有许多设计和用途，但没有一个综合的数据库包含这些实验的结果。为了解决这个问题，我们开发了MPRAbase，这是一个人工管理的数据库，目前包含130个实验，涵盖了35种细胞类型和4种生物体的17,718,677个元素。MPRAbase网络界面作为一个集中的用户友好的存储库，用于在线检查跨细胞类型和生物体的调控元件的活动，并下载MPRA数据进行独立分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genome research 生物-生化与分子生物学

CiteScore

12.40

自引率

1.40%

发文量

140

审稿时长

6 months

期刊介绍： Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.