ArticleNucleic acids research2021
Validation of human microRNA target pathways enables evaluation of target prediction tools.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Candidate MicroRNA Biomarkers in Lupus Nephritis: A Meta-analysis of Profiling Studies in Kidney, Blood and Urine Samples.Molecular diagnosis & therapy · 2023Pooled it
- Review
- Circulating miR-126 and miR-155 are associated with environmental lead exposure: A translational approach via human biomonitoring and bioinformatic networks.Toxicology reports · 2026Article
- Identification and validation of NETs-associated biomarkers in osteoporosis with diabetes.Scientific reports · 2026Article
- MicroRNA‑microbiome cross‑kingdom networks drive inflammatory bowel disease through dynamic regulatory ecosystems (Review).International journal of molecular medicine · 2026Review
- Regulation of the MAPK/ERK Pathway by miRNA-27b in Gastric Cancer: Diagnostic Implications and Therapeutic Potential of Aloin.Asia-Pacific journal of clinical oncology · 2025Article
- Expanding the immune-related targetome of miR-155-5p by integrating time-resolved RNA patterns into miRNA target prediction.RNA biology · 2025Review
- Insights into the Regulatory Roles of miRNAs in the Salivary Glands of the Soft TicksPathogens (Basel, Switzerland) · 2025Article
- miRNA-Mediated Regulation of Gene Expression During Early Activation in Jurkat Cells.bioRxiv : the preprint server for biology · 2025Article
- An imbalance between proliferation and differentiation underlies the development of microRNA-defective pineoblastoma.Genes & development · 2025Article
- Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis.BMC bioinformatics · 2025Article
- MicroRNA Gets a Mighty Award.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional-Post-Transcriptional Regulatory Cross-Talk.Biology · 2025Article
- Assessment of the Role of miR-30a-5p on the Proliferation and Apoptosis of Hair Follicle Stem Cells.Journal of cosmetic dermatology · 2025Article
- Advancing miRNA cancer research through artificial intelligence: from biomarker discovery to therapeutic targeting.Medical oncology (Northwood, London, England) · 2024Review
- Endometriosis: Molecular Pathophysiology and Recent Treatment Strategies-Comprehensive Literature Review.Pharmaceuticals (Basel, Switzerland) · 2024Review
- Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease.Experimental & molecular medicine · 2024Article
- CMC: Cancer miRNA Census - a list of cancer-related miRNA genes.Nucleic acids research · 2024Article
- The miRNA-target interactions: An underestimated intricacy.Nucleic acids research · 2024Review
- Restoring microRNA-34a overcomes acquired drug resistance and disease progression in human breast cancer cell lines via suppressing the ABCC1 gene.Breast cancer research and treatment · 2024Article
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
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