Motivation: Off-target activity commonly exists in RNA interference (RNAi) screens and often generates false positives. Existing analytic methods for addressing the off-target effects are demonstrably inadequate in RNAi confirmatory screens.#R##N##R##N#Results: Here, we present an analytic method assessing the collective activity of multiple short interfering RNAs (siRNAs) targeting a gene. Using this method, we can not only reduce the impact of off-target activities, but also evaluate the specific effect of an siRNA, thus providing information about potential off-target effects. Using in-house RNAi screens, we demonstrate that our method obtains more reasonable and sensible results than current methods such as the redundant siRNA activity (RSA) method, the RNAi gene enrichment ranking (RIGER) method, the frequency approach and the t-test.#R##N##R##N#Contact: moc.kcrem@gnahz_auhoaix#R##N##R##N#Supplementary information: Supplementary data are available at Bioinformatics online.
['Xiaohua Douglas Zhang', 'Francesca Santini', 'Raul Lacson', 'Shane Marine', 'Qian Wu', 'Luca Benetti', 'Ruojing Yang', 'Alex McCampbell', 'Joel P. Berger', 'Dawn Toolan', 'Erica Stec', 'Daniel J. Holder', 'Keith A. Soper', 'Joseph F. Heyse', 'Marc Ferrer']
cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens