ArticleGenome research2017
microRNA target prediction programs predict many false positives.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers, 2 of them syntheses that pooled it.
What it found
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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.
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.
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Who cites it
153 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia.Methods in molecular biology (Clifton, N.J.) · 2025Guideline
- MicroRNAs association with azoospermia, oligospermia, asthenozoospermia, and teratozoospermia: a systematic review.Journal of assisted reproduction and genetics · 2020Pooled it
- Differential Expression of MicroRNAs in the Mammary Gland of Lactating and Dry Murciano-Granadina Goats.Animals : an open access journal from MDPI · 2026Article
- MIR1255A regulates pathways critical for brain development, risk genes for depression and neurodevelopmental disorders.Translational psychiatry · 2026Article
- Network-based analysis reveals potential microRNA regulation of oncogenic pathways in SOX10-depleted uveal melanoma.Cellular and molecular life sciences : CMLS · 2026Article
- MicroRNAs in oncology: a translational perspective in the era of AI.Nature reviews. Clinical oncology · 2026Review
- Regulation and Interaction Among SOCS1 and SOCS3 by MicroRNAs in Multiple Sclerosis: A Review andThe Yale journal of biology and medicine · 2026Review
- microRNAs affecting development of body pigmentation in adult Drosophila melanogaster.bioRxiv : the preprint server for biology · 2026Article
- An Integrative Framework Identifies Cooperative Targeting of Host Pathways by Tick Salivary miRNAs.Computational and structural biotechnology journal · 2026Article
- Integrated miR-omics and proteomics reveal the regulatory role of miR in protein networks associated with COVID-19 disease progression.Frontiers in immunology · 2026Article
- Strongly regulated transcription factors exert an outsized influence in microRNA-regulated networks.Cell communication and signaling : CCS · 2025Article
- Ohno-miRNAs: miRNA pairs derived from whole-genome duplication.PLoS computational biology · 2025Article
- Human DICER1 hotspot mutation induces both loss and gain of miRNA function.Nature structural & molecular biology · 2025Article
- Article
- Intravenously injected hPSC-derived pericytes for Alzheimer disease: Neuroprotection and vascular repair via extracellular vesicles.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- RNACOREX - RNA coregulatory network explorer and classifier.PLoS computational biology · 2025Article
- Strong Association Between MiRNA Gene Variants and Type 2 Diabetes Mellitus in a Caucasian Population.International journal of molecular sciences · 2025Article
- Human Dicer1 hotspot mutation induces both loss and gain of miRNA function.bioRxiv : the preprint server for biology · 2025Article
- Common and distinct circulating microRNAs in four neurovascular disorders.Biochemistry and biophysics reports · 2025Article
- A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.Molecular ecology · 2025Article
93 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
According to the current view, each microRNA regulates hundreds of genes. Computational tools aim at identifying microRNA targets, usually selecting evolutionarily conserved microRNA binding sites. While the false positive rates have been evaluated for some prediction programs, that information is rarely put forward in studies making use of their predictions. Here, we provide evidence that such predictions are often biologically irrelevant. Focusing on miR-223-guided repression, we observed that it is often smaller than inter-individual variability in gene expression among wild-type mice, suggesting that most predicted targets are functionally insensitive to that microRNA. Furthermore, we found that human haplo-insufficient genes tend to bear the most highly conserved microRNA binding sites. It thus appears that biological functionality of microRNA binding sites depends on the dose-sensitivity of their host gene and that, conversely, it is unlikely that every predicted microRNA target is dose-sensitive enough to be functionally regulated by microRNAs. We also observed that some mRNAs can efficiently titrate microRNAs, providing a reason for microRNA binding site conservation for inefficiently repressed targets. Finally, many conserved microRNA binding sites are conserved in a microRNA-independent fashion: Sequence elements may be conserved for other reasons, while being fortuitously complementary to microRNAs. Collectively, our data suggest that the role of microRNAs in normal and pathological conditions has been overestimated due to the frequent overlooking of false positive rates.
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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.