ArticlePloS one2012
DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
19 citing papers in PubMed, 31 citations in OpenAlex.
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- SiaRNA: a siamese neural network with bidirectional cross-attention for pairwise siRNA-mRNA efficacy prediction.Frontiers in bioinformatics · 2026Article
- Designing siRNAs against non-structural genes of all serotypes of Dengue virus using RNAi technology - A computational investigation.Journal, genetic engineering & biotechnology · 2025Article
- HOXA13 promotes immune evasion in bladder cancer by suppressing antigen processing and presentation, and phagosome pathways.Functional & integrative genomics · 2025Article
- siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.Briefings in bioinformatics · 2024Article
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- A polycistronic transgene design for combinatorial genetic perturbations from a single transcript in Drosophila.PLoS genetics · 2023Article
- Antiviral efficacy of short-hairpin RNAs and artificial microRNAs targeting foot-and-mouth disease virus.PeerJ · 2021Article
- Protein kinase CK2 contributes to placental development: physiological and pathological implications.Journal of molecular medicine (Berlin, Germany) · 2020Article
- Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models.Frontiers in oncology · 2020Article
- ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy.G3 (Bethesda, Md.) · 2017Article
- Prediction of potent shRNAs with a sequential classification algorithm.Nature biotechnology · 2017Article
- Functional inhibition of chemokine receptor CCR2 by dicer-substrate-siRNA prevents pain development.Molecular pain · 2016Article
- Silencing efficacy prediction: a retrospective study on target mRNA features.Bioscience reports · 2015Article
- Size unbiased representative enzymatically generated RNAi (SURER) library and application for RNAi therapeutic screens.Nucleic acid therapeutics · 2015Article
- VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.Journal of translational medicine · 2013Article
- Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammalian cells. However, designing potent siRNA remains challenging. Among tools predicting siRNA efficacy, very few have been validated on endogenous targets in realistic experimental conditions. We previously described a tool to assist efficient siRNA design (DSIR, Designer of siRNA), which focuses on intrinsic features of the siRNA sequence. Here, we evaluated DSIR's performance by systematically investigating the potency of the siRNA it designs to target ten cancer-related genes. mRNA knockdown was measured by quantitative RT-PCR in cell-based assays, revealing that over 60% of siRNA sequences designed by DSIR silenced their target genes by at least 70%. Silencing efficacy was sustained even when low siRNA concentrations were used. This systematic analysis revealed in particular that, for a subset of genes, the efficiency of siRNA constructs significantly increases when the sequence is located closer to the 5'-end of the target gene coding sequence, suggesting the distance to the 5'-end as a new feature for siRNA potency prediction. A new version of DSIR incorporating these new findings, as well as the list of validated siRNA against the tested cancer genes, has been made available on the web (http://biodev.extra.cea.fr/DSIR).
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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.