ArticlePloS one2011
Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An integrative meta-analysis of microRNAs in hepatocellular carcinoma.Genomics, proteomics & bioinformatics · 2013Pooled it
- Trials and Tribulations of MicroRNA Therapeutics.International journal of molecular sciences · 2024Review
- Non-Canonical Targets of MicroRNAs: Role in Transcriptional Regulation, Disease Pathogenesis and Potential for Therapeutic Targets.MicroRNA (Shariqah, United Arab Emirates) · 2024Review
- Restoring Ravaged Heart: Molecular Mechanisms and Clinical Application of miRNA in Heart Regeneration.Frontiers in cardiovascular medicine · 2022Review
- Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy.International journal of molecular sciences · 2021Review
- The Potential for microRNA Therapeutics and Clinical Research.Frontiers in genetics · 2019Review
- mirDIP 4.1-integrative database of human microRNA target predictions.Nucleic acids research · 2018Article
- RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.Nucleic acids research · 2017Article
- miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data.Nucleic acids research · 2017Article
- Article
- MicroRNA target site identification by integrating sequence and binding information.Nature methods · 2013Article
- Advances in the techniques for the prediction of microRNA targets.International journal of molecular sciences · 2013Review
- miR-1279, miR-548j, miR-548m, and miR-548d-5p binding sites in CDSs of paralogous and orthologous PTPN12, MSH6, and ZEB1 Genes.BioMed research international · 2013Article
- Search for signatures in miRNAs associated with cancer.Bioinformation · 2013Article
- Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets.Nucleic acids research · 2012Article
- Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.BMC genomics · 2012Article
- Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis.Molecular neurobiology · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany computational microRNA target prediction tools are focused on several key features, including complementarity to 5'seed of miRNAs and evolutionary conservation. While these features allow for successful target identification, not all miRNA target sites are conserved and adhere to canonical seed complementarity. Several studies have propagated the use of energy features of mRNA:miRNA duplexes as an alternative feature. However, different independent evaluations reported conflicting results on the reliability of energy-based predictions. Here, we reassess the usefulness of energy features for mammalian target prediction, aiming to relax or eliminate the need for perfect seed matches and conservation requirement. METHODOLOGY/PRINCIPAL
findingsWe detect significant differences of energy features at experimentally supported human miRNA target sites and at genome-wide sites of AGO protein interaction. This trend is confirmed on datasets that assay the effect of miRNAs on mRNA and protein expression changes, and a simple linear regression model leads to significant correlation of predicted versus observed expression change. Compared to 6-mer seed matches as baseline, application of our energy-based model leads to ∼3-5-fold enrichment on highly down-regulated targets, and allows for prediction of strictly imperfect targets with enrichment above baseline. CONCLUSIONS/SIGNIFICANCE: In conclusion, our results indicate significant promise for energy-based miRNA target prediction that includes a broader range of targets without having to use conservation or impose stringent seed match rules.
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