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Analysis of cell-based RNAi screens

Michael Boutros1*, Lígia P Brás23 and Wolfgang Huber2*

Author Affiliations

1 Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany

2 EMBL - European Bioinformatics Institute, Cambridge CB10 1SD, UK

3 Centre for Chemical and Biological Engineering, IST, Technical University of Lisbon, Av. Rovisco Pais, P-1049-001 Lisbon, Portugal

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Genome Biology 2006, 7:R66  doi:10.1186/gb-2006-7-7-r66

Published: 25 July 2006


RNA interference (RNAi) screening is a powerful technology for functional characterization of biological pathways. Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data. It is implemented in an open-source Bioconductor/R package, cellHTS ( webcite). The method is useful for the analysis and documentation of individual RNAi screens. Moreover, it is a prerequisite for the integration of multiple experiments.