Evidence map›Paper›PMID 38617248›Full record

ArticlebioRxiv : the preprint server for biology2024

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

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

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

Article in bioRxiv : the preprint server for biology, 2024. 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, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 1 country.

Javlon NizomovDepartment of Biostatistics, University of Florida, Gainesville, FL, 32603.
Weijia JinDepartment of Biostatistics, University of Florida, Gainesville, FL, 32603.
Yi XiaDepartment of Biostatistics, University of Florida, Gainesville, FL, 32603.
Yunlong LiuDepartment of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202.ORCID 0000-0002-2699-626X
Zhigang LiDepartment of Biostatistics, University of Florida, Gainesville, FL, 32603.
Li ChenDepartment of Biostatistics, University of Florida, Gainesville, FL, 32603.ORCID 0000-0001-9372-5606
University of Florida · USUniversity School · US

Funding

Computational modeling of genetic variations by multi-omics integration todecipher personal genomeR35GM142701 · NIGMS · UNIVERSITY OF FLORIDA · PI CHEN, LI · 2021 to 2025
$1.8M
NIGMS NIH HHS R35 GM142701
6 · The paper itself

Abstract

Massively parallel reporter assay (MPRA) is an important technology to evaluate 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 various genomic features, resulting in a total of 242,818 variants tested across more than 30 cell lines and 30 human diseases or traits. MPRAVarDB empowers the query of MPRA variants by genomic region, disease and cell line or by any combination of these query terms. Notably, MPRAVarDB offers a suite of pretrained machine learning models tailored to the specific disease and cell line, facilitating the genome-wide prediction of regulatory variants. MPRAVarDB is friendly to use, and users only need a few clicks to receive query and prediction results.

Identifiers

PMID38617248
PMCPMC11014600
OpenAlexW4393902262

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.