GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update

Abstract

RNA interference (RNAi) represents a powerful method to systematically study loss-of-function phenotypes on a large scale with a wide variety of biological assays, constituting a rich source for the assignment of gene function. The GenomeRNAi database (http://www.genomernai.org) makes available RNAi phenotype data extracted from the literature for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity. This manuscript describes an update of the database previously featured in the NAR Database Issue. 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. We have added a page listing 'frequent hitters', i.e. genes that show a phenotype in many screens, which might guide on-going RNAi studies. Structured annotation guidelines have been established to facilitate consistent curation, and a submission template for direct submission by data producers is available for download.

Figure 1.

Examples of data output pages. (a) Gene details page for the human gene ELF2, Entrez Gene ID 1998. Information on a gene is arranged into four tabs; the ‘Phenotypes’ tab opens by default. A list of screens that included the respective gene is displayed, along with author-provided gene IDs, gene symbols and reagent identifiers, as well as the scores and phenotypes recorded. For numerical scores, a little image underneath indicates the distribution of the scores and the relative position of the score in question. Screen titles are hyperlinked and display more details on the screen when clicked upon. The screen ‘Combinatorial effect with paclitaxel’ recorded the phenotype ‘Decreased viability with paclitaxel’ for the ELF2 gene. For the screen ‘HeLa cell morphology’, the phenotype is given as ‘Cells with protrusions’, and for this screen the user can open an image for direct assessment of the phenotype. (b) Dynamic genome browser display for the human ELF2 gene (fourth tab). RNAi reagents and phenotypes are displayed via the DAS technology in a Dalliance browser (8). RNASeq data for three human cell lines are provided as additional tracks at the bottom. Clicking on the phenotype track opens a window with information on the genomic location, the phenotypes recorded for this gene and a link to the respective gene details page in GenomeRNAi. The user can modify the display by zooming and scrolling, and also by adding additional tracks for data sources available from the DAS registry. (c) Reagent details page for the reagent BKN51124, targeting the cdc2 gene in Drosophila. The type of reagent, source library information and the sequence of the reagent are shown. Clicking on ‘details’ next to the library name, a mouse-over window displays additional information on the source library. The library name is hyperlinked to the library provider’s website. Additional sections provide primer characteristics, a quality assessment obtained by the NEXT-RNAi software (7) as well as information on the intended target gene for the selected reagent. If applicable, off-target genes are also displayed. (d) Screen-phenotype display for a Toll pathway screen by Kuttenkeuler et al. The screen has been selected on the ‘Browse’ page, followed by clicking on the ‘View Phenotypes’ button. Some key details on the screen are shown at the top row, including the publication title, hyperlinked for additional screen information, then a short screen title, as well as details on the assay, the biomodel and the species used in the experiment. This is followed by a list of phenotypes identified in the selected screen, along with the number of entries associated with each phenotype. Upon clicking on a phenotype, a table of genes recorded as showing this phenotype opens up. This table provides a hyperlinked Entrez Gene ID for all entries that could successfully be mapped. Furthermore, it contains author-provided gene and reagent details, followed by information on score type, applied score cut-off and the score itself. The ‘Follow Up’ column indicates whether further experiments have been performed with the aim of confirming the phenotype.