A database containing phenotypes from RNA interference (RNAi) screens in Drosophila and human. In addition, the database provides an updated resource of RNAi reagents and their predicted quality. RNAi screening data is extracted from the literature by manual curation, but we also provide a functionality for direct submission by data producers. The new version has undergone a complete re-design of the user interface, providing an intuitive, flexible framework for additional functionalities. Screen information and gene-reagent-phenotype associations are now available for download. The integration with other resources has been improved by allowing in-links via GenomeRNAi screen IDs, or external gene or reagent identifiers. A distributed annotation system (DAS) server enables the visualization of the phenotypes and reagents in the context of a genome browser.
Compiles information about the red flour beetle Tribolium castaneum. iBeetle-Base gathers sequence information and links for the totality of genes of the Tribolium castaneum as well as annotations of RNAi phenotypes, described with controlled vocabularies and the Tribolium morphological ontology (TrOn). Searches can be made by specific phenotypes, gene names or IDs, and files of interest can be downloaded as an Excel, CSV or a PDF file.
Allows the identification of genetic and pharmacologic dependencies, as well as the biomarkers they are predicted by. Depmap is a preclinical reference map that provides an approach to define and predict genes that are essential for cell viability, thereby facilitating the identification of cancer targets. The database connects tumor features with tumor dependencies. It can be useful for targeted therapeutic development.
Serves a dual role, tracking both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. FlyRNAi is used as a platform for community availability of protocols, tools, and other resources useful to researchers planning, conducting, analyzing or interpreting the results of Drosophila RNAi screens.
Contains a compendium of publicly available data and provides information on experimental methods and phenotypic results, including raw data in the form of images and streaming time‐lapse movies. Phenotypic summaries together with graphical displays of RNAi to gene mappings allow quick intuitive comparison of results from different RNAi assays and visualization of the gene product(s) potentially inhibited by each RNAi experiment based on multiple sequence analysis methods. RNAiDB can be searched using combinatorial queries and using the novel tool PhenoBlast, which ranks genes according to their overall phenotypic similarity. RNAiDB could serve as a model database for distributing and navigating in vivo functional information from large‐scale systematic phenotypic analyses in different organisms.
An online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and data-mining in Drosophila.
Contains validation information about published small inferring RNA (siRNA) sequences. sIR is an online repository that offers users an interface for analyzing and designing siRNA sequences against a chosen target sequence. It includes a weighted scoring system to predict siRNA efficacy, and has four modes: the target design mode, the accession finder mode, the siRNA resource mode and the pre-computed siRNA database mode.