We have developed a range of computational tools for the analysis of screening data sets. This includes a web application providing a graphical interface to cellHTS2, GenomeRNAi, a database for RNAi screening results, E-RNAi for the design and evaluation of RNAi reagents and NEXT-RNAi for the design and evaluation of genome-wide RNAi libraries.
High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify phenotypic hits. The web application, a front-end to the Bioconductor/R package cellHTS2, guides the user through all configuration steps required for analysis of single or multi-channel experiments. The web-application provides various options for standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and re-stored for later re-analysis.
Link to documentation and tutorial: web-cellHTS2
The GenomeRNAi database contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. The availability of phenotypes from Drosophila and human screens also allows for phenotype searches across species. Besides reporting quantitative data from genome-scale screens, GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome.
Web site: GenomeRNAi
For the correct assessment of phenotypes, a key issue remains the stringent quality control of long double-stranded RNAs (dsRNA) to calculate potential off-target effects that may obscure the phenotypic data. We have developed a web-based tool to evaluate and design optimized dsRNA constructs.
Web site: E-RNAi
NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries and performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context. The software enables the design and evaluation of siRNAs and long dsRNAs and was implemented in an organism-independent manner allowing designs for all sequenced and annotated genomes. It requires the minimal input of desired target sequences and an off-target database.
NEXT-RNAi implements several methods to predict a reagents' quality and offers many special features such as the straight-forward design of independent RNAi reagents.
Web site: Next-RNAi