title: cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  xiaohua_zhang@merck.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Biometrics Research, Merck Research Laboratories, West Point, PA 19486, USA. xiaohua_zhang@merck.com
authors.forename: Xiaohua Douglas
authors.initials: XD
authors.lastname: Zhang
authors.forename: Francesca
authors.initials: F
authors.lastname: Santini
authors.forename: Raul
authors.initials: R
authors.lastname: Lacson
authors.forename: Shane D
authors.initials: SD
authors.lastname: Marine
authors.forename: Qian
authors.initials: Q
authors.lastname: Wu
authors.forename: Luca
authors.initials: L
authors.lastname: Benetti
authors.forename: Ruojing
authors.initials: R
authors.lastname: Yang
authors.forename: Alex
authors.initials: A
authors.lastname: McCampbell
authors.forename: Joel P
authors.initials: JP
authors.lastname: Berger
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Toolan
authors.forename: Erica M
authors.initials: EM
authors.lastname: Stec
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Holder
authors.forename: Keith A
authors.initials: KA
authors.lastname: Soper
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Heyse
authors.forename: Marc
authors.initials: M
authors.lastname: Ferrer
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D003627:Data Interpretation, Statistical; D003920:Diabetes Mellitus / Q000235:genetics; D055785:Gene Knockdown Techniques; D023281:Genomics / Q000379:methods; D014645:Herpesvirus 3, Human / Q000235:genetics; D057166:High-Throughput Screening Assays; D006801:Humans; D034622:RNA Interference; D034741:RNA, Small Interfering
chemical_list: D034741:RNA, Small Interfering