Evidence map›Paper›PMID 38045264›Full record

ArticlebioRxiv : the preprint server for biology2023

MPRAbase: A Massively Parallel Reporter Assay Database.

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

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 7 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 5 institutions in 3 countries.

Jingjing ZhaoDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.
Fotis A BaltoumasInstitute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, 16672, Greece.
Maxwell A KonnarisInstitute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Ioannis MouratidisInstitute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
Zhe LiuDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.
Jasmine SimsDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.
Vikram AgarwalmRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA.ORCID 0000-0001-8148-952X
Georgios A PavlopoulosInstitute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, 16672, Greece.
Ilias Georgakopoulos-SoaresInstitute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.ORCID 0000-0003-3641-1488
Nadav AhituvDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.
Pennsylvania State University · USUniversity of California, San Francisco · USAlexander Fleming Biomedical Sciences Research Center · GRCity University of Hong Kong · HKSanofi (United States) · US

Funding

Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systemsUM1HG011966 · NHGRI · UNIVERSITY OF WASHINGTON · PI Nadav Ahituv, Jay Ashok Shendure · 2021 to 2026
$9.7M
Massively parallel reporter assays and genome editing of ENCODE predicted regulatory elementsUM1HG009408 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2017 to 2021
$7.6M
Harnessing the Power of Kmers: Concepts and Methods for Genomic and Proteomic ResearchR35GM155468 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI Ilias Georgakopoulos-Soares · 2024 to 2026
$1.2M
NHGRI NIH HHS UM1 HG009408NHGRI NIH HHS UM1 HG011966NIGMS NIH HHS R35 GM155468
6 · The paper itself

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 129 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface (http://www.mprabase.com) serves as a centralized user-friendly repository to download existing MPRA data for independent analysis and is designed with the ability to allow researchers to share their published data for rapid dissemination to the community.

Identifiers

PMID38045264
PMCPMC10690217
OpenAlexW4388928668

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.