Evidence map›Paper›PMID 38469560›Full record

ArticleiScience2024

sRNA-Effector: A tool to expedite discovery of small RNA regulators.

Briana Wilson, Fatemeh Esmaeili, Matthew Parsons, Wafa Salah, Zhangli Su, Anindya Dutta

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 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, top 98% of its field
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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 1 country.

Briana WilsonDepartment of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
Fatemeh EsmaeiliDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
Matthew ParsonsDepartment of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
Wafa SalahDepartment of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
Zhangli SuDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
Anindya DuttaDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
University of Alabama at Birmingham · USUniversity of Virginia · US

Funding

Women's Oncology Program - WONP30CA044579 · NCI · UNIVERSITY OF VIRGINIA CHARLOTTESVILLE · PI Jay William FOX · 1987 to 2026
$72.1M
The role of MCM8-9 in genomic instability of cancersR01CA060499 · NCI · UNIVERSITY OF VIRGINIA CHARLOTTESVILLE · PI Anindya Dutta · 1994 to 2026
$8.6M
Involvement of Noncanonical Short RNAs in Gene Repression through the RNA-Induced-Silencing ComplexR01GM146756 · NIGMS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI DUTTA, ANINDYA · 2022 to 2025
$1.3M
The role of small RNA modifications in gliomaR00CA259526 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI SU, ZHANGLI · 2023 to 2025
$708k
Stability of a novel family of short noncoding RNAs, tRFs: Effect on oncogenesisF30CA254134 · NCI · UNIVERSITY OF VIRGINIA · PI WILSON, BRIANA · 2020 to 2022
$120k
NCI NIH HHS F30 CA254134NCI NIH HHS P30 CA044579NCI NIH HHS R00 CA259526NCI NIH HHS R01 CA060499NIGMS NIH HHS R01 GM146756
6 · The paper itself

Abstract

microRNAs (miRNAs) are small regulatory RNAs that repress target mRNA transcripts through base pairing. Although the mechanisms of miRNA production and function are clearly established, new insights into miRNA regulation or miRNA-mediated gene silencing are still emerging. In order to facilitate the discovery of miRNA regulators or effectors, we have developed sRNA-Effector, a machine learning algorithm trained on enhanced crosslinking and immunoprecipitation sequencing and RNA sequencing data following knockdown of specific genes. sRNA-Effector can accurately identify known miRNA biogenesis and effector proteins and identifies 9 putative regulators of miRNA function, including serine/threonine kinase STK33, splicing factor SFPQ, and proto-oncogene BMI1. We validated the role of STK33, SFPQ, and BMI1 in miRNA regulation, showing that sRNA-Effector is useful for identifying new players in small RNA biology. sRNA-Effector will be a web tool available for all researchers to identify potential miRNA regulators in any cell line of interest.

Indexed as

Biocomputational methodGene networkMachine learningNucleic acids

Identifiers

PMID38469560
PMCPMC10926228
OpenAlexW4391966641

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.