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. 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. CONTACT: xiaohua_zhang@merck.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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. 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. CONTACT: xiaohua_zhang@merck.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Xiaohua Douglas Zhang; Raul Lacson; Ruojing Yang; Shane D Marine; Alex McCampbell; Dawn M Toolan; Tim R Hare; Joleen Kajdas; Joel P Berger; Daniel J Holder; Joseph F Heyse; Marc Ferrer Journal: J Biomol Screen Date: 2010-09-17
Authors: Xiaohua Douglas Zhang; Marc Ferrer; Amy S Espeseth; Shane Douglas Marine; Erica M Stec; Michael A Crackower; Daniel J Holder; Joseph F Heyse; Berta Strulovici Journal: J Biomol Screen Date: 2007-04-13
Authors: Wei-Qin Zhao; Francesca Santini; Robert Breese; Dave Ross; Xiaohua Douglas Zhang; David J Stone; Marc Ferrer; Matthew Townsend; Abigail L Wolfe; Matthew A Seager; Gene G Kinney; Paul J Shughrue; William J Ray Journal: J Biol Chem Date: 2009-12-23 Impact factor: 5.157
Authors: David A Barbie; Pablo Tamayo; Jesse S Boehm; So Young Kim; Susan E Moody; Ian F Dunn; Anna C Schinzel; Peter Sandy; Etienne Meylan; Claudia Scholl; Stefan Fröhling; Edmond M Chan; Martin L Sos; Kathrin Michel; Craig Mermel; Serena J Silver; Barbara A Weir; Jan H Reiling; Qing Sheng; Piyush B Gupta; Raymond C Wadlow; Hanh Le; Sebastian Hoersch; Ben S Wittner; Sridhar Ramaswamy; David M Livingston; David M Sabatini; Matthew Meyerson; Roman K Thomas; Eric S Lander; Jill P Mesirov; David E Root; D Gary Gilliland; Tyler Jacks; William C Hahn Journal: Nature Date: 2009-10-21 Impact factor: 49.962
Authors: Richard A Klinghoffer; Jason Frazier; James Annis; Jason D Berndt; Brian S Roberts; William T Arthur; Raul Lacson; Xiaohua Douglas Zhang; Marc Ferrer; Randall T Moon; Michele A Cleary Journal: PLoS One Date: 2009-09-03 Impact factor: 3.240
Authors: Aviad Tsherniak; Francisca Vazquez; Phil G Montgomery; Barbara A Weir; Gregory Kryukov; Glenn S Cowley; Stanley Gill; William F Harrington; Sasha Pantel; John M Krill-Burger; Robin M Meyers; Levi Ali; Amy Goodale; Yenarae Lee; Guozhi Jiang; Jessica Hsiao; William F J Gerath; Sara Howell; Erin Merkel; Mahmoud Ghandi; Levi A Garraway; David E Root; Todd R Golub; Jesse S Boehm; William C Hahn Journal: Cell Date: 2017-07-27 Impact factor: 41.582
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Authors: Luiz Miguel Camargo; Xiaohua Douglas Zhang; Patrick Loerch; Ramon Miguel Caceres; Shane D Marine; Paolo Uva; Marc Ferrer; Emanuele de Rinaldis; David J Stone; John Majercak; William J Ray; Chen Yi-An; Mark S Shearman; Kenji Mizuguchi Journal: PLoS One Date: 2015-02-27 Impact factor: 3.240
Authors: Alexander Karlas; Stefano Berre; Thérèse Couderc; Margus Varjak; Peter Braun; Michael Meyer; Nicolas Gangneux; Liis Karo-Astover; Friderike Weege; Martin Raftery; Günther Schönrich; Uwe Klemm; Anne Wurzlbauer; Franz Bracher; Andres Merits; Thomas F Meyer; Marc Lecuit Journal: Nat Commun Date: 2016-05-12 Impact factor: 14.919
Authors: Ryan L Boudreau; Ryan M Spengler; Ray H Hylock; Brandyn J Kusenda; Heather A Davis; David A Eichmann; Beverly L Davidson Journal: Nucleic Acids Res Date: 2012-08-31 Impact factor: 16.971