ArticleBMC bioinformatics2006
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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
20 citing papers in PubMed.
- siRNA Design and GalNAc-Empowered Hepatic Targeted Delivery.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A database of breast oncogenic specific siRNAs.Scientific reports · 2017Article
- A semi-supervised tensor regression model for siRNA efficacy prediction.BMC bioinformatics · 2015Article
- Computational design of artificial RNA molecules for gene regulation.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Target gene abundance contributes to the efficiency of siRNA-mediated gene silencing.Nucleic acid therapeutics · 2014Article
- Design of siRNA Therapeutics from the Molecular Scale.Pharmaceuticals (Basel, Switzerland) · 2013Article
- Mini-clusters with mean probabilities for identifying effective siRNAs.BMC research notes · 2012Article
- Optimized models for design of efficient miR30-based shRNAs.Frontiers in genetics · 2012Article
- Reconsideration of in-silico siRNA design based on feature selection: a cross-platform data integration perspective.PloS one · 2012Article
- shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction.Bioinformation · 2012Article
- Article
- Nicotinamide adenine dinucleotide (NAD)-regulated DNA methylation alters CCCTC-binding factor (CTCF)/cohesin binding and transcription at the BDNF locus.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Article
- Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study.BMC bioinformatics · 2010Article
- Article
- Simple construction of plant RNAi vectors using long oligonucleotides.Journal of plant research · 2009Article
- Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency.Bioinformatics (Oxford, England) · 2009Article
- Prediction of guide strand of microRNAs from its sequence and secondary structure.BMC bioinformatics · 2009Article
- siRecords: a database of mammalian RNAi experiments and efficacies.Nucleic acids research · 2009Article
- Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundShort interfering RNAs have allowed the development of clean and easily regulated methods for disruption of gene expression. However, while these methods continue to grow in popularity, designing effective siRNA experiments can be challenging. The various existing siRNA design guidelines suffer from two problems: they differ considerably from each other, and they produce high levels of false-positive predictions when tested on data of independent origins.
resultsUsing a distinctly large set of siRNA efficacy data assembled from a vast diversity of origins (the siRecords data, containing records of 3,277 siRNA experiments targeting 1,518 genes, derived from 1,417 independent studies), we conducted extensive analyses of all known features that have been implicated in increasing RNAi effectiveness. A number of features having positive impacts on siRNA efficacy were identified. By performing quantitative analyses on cooperative effects among these features, then applying a disjunctive rule merging (DRM) algorithm, we developed a bundle of siRNA design rule sets with the false positive problem well curbed. A comparison with 15 online siRNA design tools indicated that some of the rule sets we developed surpassed all of these design tools commonly used in siRNA design practice in positive predictive values (PPVs).
conclusionThe availability of the large and diverse siRNA dataset from siRecords and the approach we describe in this report have allowed the development of highly effective and generally applicable siRNA design rule sets. Together with ever improving RNAi lab techniques, these design rule sets are expected to make siRNAs a more useful tool for molecular genetics, functional genomics, and drug discovery studies.
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