ArticleBioinformatics (Oxford, England)2015
Bias in microRNA functional enrichment analysis.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
78 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders.PloS one · 2023Pooled it
- MicroRNA meta-signature of oral cancer: evidence from a meta-analysis.Upsala journal of medical sciences · 2018Pooled it
- Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma.Human molecular genetics · 2018Trial
- Conserved Core and Species-Specific Signatures in the Milk Exosomal microRNA Targetome: A Preliminary Comparative In Silico Analysis of Human, Cow, Goat and Donkey Milk.International journal of molecular sciences · 2026Article
- Peripheral microRNA signature in genetic frontotemporal dementia-findings from the GENFI initiative.GeroScience · 2026Article
- Functional properties of skeletal myotube-derived extracellular vesicles based on microRNA profiles: a comparative analysis with mesenchymal stem cell-derived extracellular vesicles.Scientific reports · 2026Article
- Circulating MicroRNAs do not provide a diagnostic benefit over tissue biopsy in patients with brain metastases.Scientific reports · 2025Article
- Plasma-Derived Extracellular Vesicle-Propagated microRNA From Aortic Stenosis Patients Render Pro-Calcifying Effects on Valve Interstitial Cells.JACC. Basic to translational science · 2025Article
- Combination of CRP and miRNA signature as a potential diagnostic strategy for Kawasaki disease.Frontiers in pediatrics · 2025Article
- An Overview of miRNA and miRNA Target Analysis Tools.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Advancing outcome measure development and analytical approaches: Pain in Animals Workshop 2023.Frontiers in pain research (Lausanne, Switzerland) · 2025Review
- Evaluating the performance of multi-omics integration: a thyroid toxicity case study.Archives of toxicology · 2025Article
- A new perspective on microRNA-guided gene regulation specificity, and its potential generalization to transcription factors and RNA-binding proteins.Nucleic acids research · 2024Review
- ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation.International journal of molecular sciences · 2024Article
- A dynamic microRNA profile that tracks a chemotherapy resistance phenotype in osteosarcoma. Implications for novel therapeutics.medRxiv : the preprint server for health sciences · 2024Article
- Donor Sites and Harvesting Techniques Affect miRNA Cargos of Extracellular Vesicles Released by Human Adipose-Derived Mesenchymal Stromal Cells.International journal of molecular sciences · 2024Article
- MHIF-MSEA: a novel model of miRNA set enrichment analysis based on multi-source heterogeneous information fusion.Frontiers in genetics · 2024Article
- Altered Extracellular Vesicle miRNA Profile in Prodromal Alzheimer's Disease.International journal of molecular sciences · 2023Article
- PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.Briefings in bioinformatics · 2023Article
- DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts.Nucleic acids research · 2023Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMany studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional categories, many of which appear frequently in the analysis of apparently unrelated diseases and conditions.
resultsWe show that the most commonly used functional enrichment test is inappropriate for the analysis of sets of genes targeted by miRNAs. The hypergeometric distribution used by the standard method consistently results in significant P-values for functional enrichment for targets of randomly selected miRNAs, reflecting an underlying bias in the predicted gene targets of miRNAs as a whole. We developed an algorithm to measure enrichment using an empirical sampling approach, and applied this in a reanalysis of the gene ontology classes of targets of miRNA lists from 44 published studies. The vast majority of the miRNA target sets were not significantly enriched in any functional category after correction for bias. We therefore argue against continued use of the standard functional enrichment method for miRNA targets.
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