ArticleNucleic acids research2015
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 69 citations in OpenAlex.
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- Determinants of Functional MicroRNA Targeting.Molecules and cells · 2023Review
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- Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists.Computational and structural biotechnology journal · 2021Review
- miRNA Targets: From Prediction Tools to Experimental Validation.Methods and protocols · 2020Review
- MicroRNAs in ascending thoracic aortic aneurysms.Bioscience reports · 2020Observational
- Population variation in miRNAs and isomiRs and their impact on human immunity to infection.Genome biology · 2020Article
- RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction.Scientific reports · 2020Article
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals.Bioinformatics (Oxford, England) · 2020Article
- The biochemical basis of microRNA targeting efficacy.Science (New York, N.Y.) · 2019Article
- Altered microRNA and target gene expression related to Tetralogy of Fallot.Scientific reports · 2019Article
- Challenges in microRNAs' targetome prediction and validation.Neural regeneration research · 2019Article
- Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data.Genome biology · 2019Article
- Comprehensive Analysis of Human microRNA-mRNA Interactome.Frontiers in genetics · 2019Article
- Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.Molecular systems biology · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small interfering RNA (siRNA)-mediated knock-down is a widely used experimental approach to characterizing gene function. Although siRNAs are designed to guide the cleavage of perfectly complementary mRNA targets, acting similarly to microRNAs (miRNAs), siRNAs down-regulate the expression of hundreds of genes to which they have only partial complementarity. Prediction of these siRNA 'off-targets' remains difficult, due to the incomplete understanding of siRNA/miRNA-target interactions. Combining a biophysical model of miRNA-target interaction with structure and sequence features of putative target sites we developed a suite of algorithms, MIRZA-G, for the prediction of miRNA targets and siRNA off-targets on a genome-wide scale. The MIRZA-G variant that uses evolutionary conservation performs better than currently available methods in predicting canonical miRNA target sites and in addition, it predicts non-canonical miRNA target sites with similarly high accuracy. Furthermore, MIRZA-G variants predict siRNA off-target sites with an accuracy unmatched by currently available programs. Thus, MIRZA-G may prove instrumental in the analysis of data resulting from large-scale siRNA screens.
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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.