Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

Using 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).The 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.Short interfering RNAs (siRNAs) are double-stranded RNAs typically of length between 19 and 25 with 2 nucleotide overhangs on the 3' ends, and they are capable of inducing sequence-specific, post-transcriptional deletion of gene products, leading to the silencing of the gene activity. Naturally occurring siRNAs are cleavage products from long double-stranded RNAs (dsRNAs) by Dicer, a ribonuclease III enzyme [1,2]. The siRNA-induced mRNA degradation is a complicated process involving multiple steps, initiated by the binding of siRNA with RISC (RNA induced silencing complex), followed by RISC's activation, resulting in the recognition of the target mRNA and the degradation of the latter [1,3,4]. As a gene knock-down tool used