Analysis of cell-based RNAi screens
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
Genome Biology 2006, 7:R66 doi:10.1186/gb-2006-7-7-r66Published: 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 (http://www.dkfz.de/signaling/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.