RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity

S Mazur,G Csucs,K Kozak

doi:10.1093/database/bas027

Abstract

Large-scale RNA interference (RNAi) experiments, especially the ones based on short-interfering RNA (siRNA) technology became increasingly popular over the past years. For such knock-down/screening purposes, different companies offer sets of oligos/reagents targeting the whole genome or a subset of it for various organisms. Obviously, the sequence (and structure) of the corresponding oligos is a key factor in obtaining reliable results in these large-scale studies and the companies use a variety of (often not fully public) algorithms to design them. Nevertheless, as the genome annotations are still continuously changing, oligos may become obsolete, so siRNA reagents should be periodically re-annotated according to the latest version of the sequence database (which of course has serious consequences also on the interpretation of the screening results). In our article, we would like to introduce a new software/database tool, the RNAiAtlas. It has been created for exploration, analysis and distribution of large scale RNAi libraries (currently limited to the human genome) with their latest annotation (including former history) but in addition it contains also specific on-target analysis results (design quality, side effects, off-targets).Database URL: http://www.rnaiatlas.ethz.ch

Highlights

RNA interference (RNAi), a natural mechanism for gene silencing [1,2], has made its way as a widely used method in molecular and cell biology in both academics and industry
Pharmaceutical and biotech companies have set up libraries for large-scale screens employing thousands of short-interfering RNAs- or short hairpin RNA(shRNA) encoding vectors to identify new factors involved in the molecular pathways of diseases [3]
The advantage of the Seed-Motif-Search for on-target analysis is that it limits the results to those genes which perfectly match with the seed region of the short-interfering RNA (siRNA)

Summary

Introduction

RNA interference (RNAi), a natural mechanism for gene silencing [1,2], has made its way as a widely used method in molecular and cell biology in both academics and industry. (beginning of 2012) the database contains 19 601 human genes including information about the three commercial siRNA libraries, such as sequence information, analyzed target specificity and predicted efficiency [10]. The graphical representation of the network of siRNA to off-target gene connections provides a powerful tool for knock-down linkage analysis, facilitating the interpretation of siRNA screening results.

Results

Conclusion