Schmidt, EE., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., and Boutros, M.
German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, D-69120 Heidelberg, Germany
GenomeRNAi collects and makes available RNA interference (RNAi) reagent and phenotype data (1,2). The database is populated by manual curation of large-scale RNAi screening experiments reported in literature for human and Drosophila. Direct submission by data producers is encouraged, and a submission template is provided for download on the website. To ensure consistency and comparability of the data, we have developed structured annotation guidelines, defining controlled vocabularies wherever possible. As of release 9 the database contains 127 screens in human, and 170 screens in Drosophila, 53 of which have been performed in vivo. The number of phenotype entries amounts to more than 500,000, ranging from quantitative biochemical readouts to complex phenotype descriptions of in vivo experiments. In addition, the database stores reagent details on more than 460,000 reagents from 14 RNAi libraries. Reagents, for which sequence information is available, are regularly assessed as to their specificity and efficiency, and are re-mapped to the current genomic sequence using the NEXT-RNAi software (3). The database is accessible via a user-friendly web interface, which allows browsing through all screens, or searching by gene name or identifier, reagent identifier or phenotype term, as well as downloading individual or bulk files with gene-reagent-phenotype associations. RNAi loss-of-function phenotypes constitute a valuable source for functional gene annotation, provided the data are well integrated with relevant gene catalogues. GenomeRNAi data are linked to a number of publically available web resources, such as Ensembl, RefSeq, OMIM, etc. Mutual web links have been established with FlyBase, UniProt and GeneCards, and GenomeRNAi data are available as data source in FlyMine.
We have recently added a â€œFrequent Hittersâ€ page, listing genes in descending order with respect to the number of times they have shown a phenotype. This might help in identifying genes with a central â€œhubâ€ function, or it might also indicate off-target effects of the RNAi reagents used. The frequent hitter list is available for download. A Distributed Annotation System (DAS) server (4) has been implemented for reagents and phenotypes included in GenomeRNAi. This allows the user to view RNAi data in the context of a genome browser, such as Ensembl. On the GenomeRNAi gene and reagent detail pages, we have also set up an interactive genome browser based on the Dalliance technology (5), providing access to GenomeRNAi and other tracks available from the DAS registry (6), along with RNASeq data from several human and Drosophila cell lines to assess expression in the region.
We thank Klaus Yserentant, Arunraj Dhamodaran, Maximilian Koch and Andreas Kling for excellent support. This project was supported by the European Communityâ€™s Seventh Framework Programme FP7/2007-2013 (CancerPathways) and the Helmholtz Alliance for Systems Biology.
1. Horn, T., Arziman, Z., Berger, J. and Boutros, M. (2007) GenomeRNAi: a database for cell-based RNAi phenotypes. Nucleic Acids Res, 35, D492-497.
2. Gilsdorf, M., Horn, T., Arziman, Z., Pelz, O., Kiner, E. and Boutros, M. (2010) GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. Nucleic Acids Res, 38, D448-452.
3. Horn, T., Sandmann, T. and Boutros, M. (2010) Design and evaluation of genome-wide libraries for RNA interference screens. Genome Biol, 11, R61.
4. Jenkinson, A.M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R.D., Hermjakob, H., Hubbard, T.J., Jimenez, R.C., Jones, P. et al. (2008) Integrating biological data--the Distributed Annotation System. BMC Bioinformatics, 9 Suppl 8, S3.
5. Down, T.A., Piipari, M. and Hubbard, T.J. (2011) Dalliance: interactive genome viewing on the web. Bioinformatics, 27, 889-890.
6. Prlic, A., Down, T.A., Kulesha, E., Finn, R.D., Kahari, A. and Hubbard, T.J. (2007) Integrating sequence and structural biology with DAS. BMC Bioinformatics, 8, 333.