Evidence map›Paper›PMID 41009792›Full record

SynthesisInternational journal of molecular sciences2025

Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.

Karolina A Biełło, José V Die, Francisco Amil, Carlos Fuentes-Almagro, Javier Pérez-Rodríguez, Alfonso Olaya-Abril

Abstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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.

Karolina A BiełłoDepartment of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, 14071 Córdoba, Spain.
José V DieDepartment of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, 14071 Córdoba, Spain.ORCID 0000-0002-7506-8590
Francisco AmilCentral Research Support Service (SCAI), Bioinformatics Unit, Rabanales de Campus, 14071 Córdoba, Spain.ORCID 0000-0002-3470-0860
Carlos Fuentes-AlmagroCentral Research Support Service (SCAI), Proteomics Unit, Rabanales de Campus, 14071 Córdoba, Spain.
Javier Pérez-RodríguezDepartment of Computer Science and Artificial Intelligence, Campus de Rabanales, 14071 Córdoba, Spain.
Alfonso Olaya-AbrilDepartment of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, 14071 Córdoba, Spain.ORCID 0000-0002-8961-1099

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Quantitative proteomics relies on robust statistical methods for differential expression, critically impacting downstream functional enrichment. This meta-analysis systematically investigated how statistical hypothesis testing approaches and criteria for defining biological relevance influence functional enrichment concordance. We reanalyzed five independent label-free quantitative proteomics datasets using diverse frequentist (

Indexed as

ProteomicsBayes TheoremComputational BiologyGene OntologyHumansReproducibility of Resultsfunctional enrichmentmeta-analysisproteomicsreproducibilitystatistical methods

Identifiers

PMID41009792
PMCPMC12471179

What Socratic holds

Textmetadata
LicenceCC BY
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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 Socratic graph.