Evidence map›Paper›PMID 39071300›Full record

ArticlebioRxiv : the preprint server for biology2024

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs.

Andrea M Baran, Arun H Patil, Ernesto Aparicio-Puerta, Marc K Halushka, Matthew N McCall

Abstract 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.

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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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Andrea M BaranDepartment of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Box 630, Rochester, NY 14642, USA.
Arun H PatilLieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe St. Suite 300, Baltimore, MD 21205, USA.
Ernesto Aparicio-PuertaDepartment of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Box 630, Rochester, NY 14642, USA.
Marc K HalushkaDepartment of Pathology, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH 44195, USA.
Matthew N McCallDepartment of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., Box 630, Rochester, NY 14642, USA.ORCID 0000-0002-2473-0943

Funding

VISUAL INDICES OF NEUROTOXICITYP30ES001247 · NIEHS · UNIVERSITY OF ROCHESTER · PI Martha Susiarjo · 1985 to 2026
$42.8M
Statistical Methods for MicroRNA-Seq ExperimentsR01GM139928 · NIGMS · UNIVERSITY OF ROCHESTER · PI MCCALL, MATTHEW NICHOLSON · 2020 to 2024
$2.0M
NIEHS NIH HHS P30 ES001247NIGMS NIH HHS R01 GM139928
6 · The paper itself

Abstract

MicroRNA-seq data is produced by aligning small RNA sequencing reads of different miRNA transcript isoforms, called isomiRs, to known microRNAs. Aggregation to microRNA-level counts discards information and violates core assumptions of differential expression (DE) methods developed for mRNA-seq data. We establish miRglmm, a DE method for microRNA-seq data, that uses a generalized linear mixed model of isomiR-level counts, facilitating detection of miRNA with differential expression or differential isomiR usage. We demonstrate that miRglmm outperforms current DE methods in estimating DE for miRNA, whether or not there is significant isomiR variability, and simultaneously provides estimates of isomiR-level DE.

Indexed as

aggregationdifferential expressionisomiRmicroRNAmiRNA-seqmixed model

Identifiers

PMID39071300
PMCPMC11275874

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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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.