ArticleNucleic acids research2015
Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis 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
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders.PloS one · 2023Pooled it
- Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma.Human molecular genetics · 2018Trial
- The role of microRNAs in executive functions: a comprehensive review and bioinformatics analysis of human and animal studies.Molecular psychiatry · 2026Review
- Circulating microRNA expression underlying the association of opioid use with low bone mineral density.JBMR plus · 2026Article
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- Article
- Quantifying the massive pleiotropy of microRNA: a human microRNA-disease causal association database generated with ChatGPT.bioRxiv : the preprint server for biology · 2024Article
- Article
- MHIF-MSEA: a novel model of miRNA set enrichment analysis based on multi-source heterogeneous information fusion.Frontiers in genetics · 2024Article
- PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.Briefings in bioinformatics · 2023Article
- The dysregulation of miRNAs in epilepsy and their regulatory role in inflammation and apoptosis.Functional & integrative genomics · 2023Review
- miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations.Nucleic acids research · 2023Article
- Comprehensive Transcriptomics Profiling of MicroRNA Reveals Plasma Circulating Biomarkers of Hypertrophic Cardiomyopathy and Dysregulated Signaling Pathways.Circulation. Heart failure · 2023Article
- MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders.Biomedicines · 2023Article
- Circulating miR-320a-3p and miR-483-5p level associated with pharmacokinetic-pharmacodynamic profiles of rivaroxaban.Human genomics · 2022Article
- Deciphering the Molecular Mechanism of Incurable Muscle Disease by a Novel Method for the Interpretation of miRNA Dysregulation.Non-coding RNA · 2022Article
- Functional Enrichment Analysis of Regulatory Elements.Biomedicines · 2022Article
- Lymphocyte Immune Response and T Cell Differentiation in Fontan Patients with protein-losing enteropathy.The Thoracic and cardiovascular surgeon · 2021Article
- Deletion of pancreas-specific miR-216a reduces beta-cell mass and inhibits pancreatic cancer progression in mice.Cell reports. Medicine · 2021Article
- Simulated Microgravity Effects on Human Adenocarcinoma Alveolar Epithelial Cells: Characterization of Morphological, Functional, and Epigenetic Parameters.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods.
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Registered trials
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.