cSSMD: Assessing collective activity for addressing off-target effects in genome-scale RNA interference screens

Bioinformatics

Volumn 27, Issue 20, 2011, Pages 2775-2781

  Zhang, Xiaohua Douglas ^a   Santini, Francesca ^a   Lacson, Raul ^a   Marine, Shane D ^a   Wu, Qian ^b   Benetti, Luca ^a   Yang, Ruojing ^a   McCampbell, Alex ^a   Berger, Joel P ^a   Toolan, Dawn M ^a   Stec, Erica M ^a   Holder, Daniel J ^a   Soper, Keith A ^a   Heyse, Joseph F ^a   Ferrer, Marc ^c  

^a MERCK RESEARCH LABORATORIES   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ALZHEIMER DISEASE; ARTICLE; DIABETES MELLITUS; EVALUATION; GENE SILENCING; GENETICS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; METHODOLOGY; RNA INTERFERENCE; STATISTICAL ANALYSIS; VARICELLA ZOSTER VIRUS;

ALZHEIMER DISEASE; DATA INTERPRETATION, STATISTICAL; DIABETES MELLITUS; GENE KNOCKDOWN TECHNIQUES; GENOMICS; HERPESVIRUS 3, HUMAN; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 80053971297     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr474     Document Type: Article

References (25)

1. Barbie, D.A. et al. (2009) Systematic RNA interference reveals that oncogenic KRASdriven cancers require TBK1. Nature, 462, 108-122.
2. Bard, F. et al. (2006) Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature, 439, 604-607.
3. Birmingham, A. et al. (2006) 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat. Methods, 3, 199-204.
4. Blow, N. (2008) RNAi technologies: a screen whose time has arrived. Nat. Methods, 5, 361-366.
5. Brass, A.L. et al. (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science, 319, 921-926.
6. Echeverri, C.J. et al. (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat. Methods, 3, 777-779.
7. Elbashir, S.M. et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNAinterference in cultured mammalian cells. Nature, 411, 494-498.
8. Glaser, V. and Ferrer, M. (2010) Interview with Marc Ferrer, Ph.D. Assay Drug Dev. Technol., 8, 263-267.
9. Jackson, A.L. et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol., 21, 635-637.
10. Klinghoffer, R.A. et al. (2009) A lentivirus-mediated genetic screen identifies dihydrofolate reductase (DHFR) as a modulator of beta-catenin/GSK3 signaling. PLoS ONE, 4.
11. Konig, R. et al. (2007)Aprobability-based approach for the analysis of large-scale RNAi screens. Nat. Methods, 4, 847-849.
12. Konig, R. et al. (2008) Global analysis of host-pathogen interactions that regulate earlystage HIV-1 replication. Cell, 135, 49-60.
13. Nybakken, K. et al. (2005) A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat. Genet., 37, 1323-1332.
14. Pelkmans, L. et al. (2005) Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature, 436, 78-86.
15. Zhang, J. (2002) Powerful goodness-of-fit tests based on the likelihood ratio. J. R. Stat. Soc. Ser. B Stat. Methodol., 64, 281-294.
16. Zhang, X.H.D. (2007) A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays. J. Biomol. Screen., 12, 645-655.
17. Zhang, X.H.D. (2008) Genome-wide screens for effective siRNAs through assessing the size of siRNA effects. BMC Res. Notes, 1, 33.
18. Zhang, X.H.D. (2009) A method for effectively comparing gene effects in multiple conditions in RNAi and expression-profiling research. Pharmacogenomics, 10, 345-358.
19. Zhang, X.H.D. (2010a) An effective method for controlling false discovery and false non-discovery rates in genome-scale RNAi screens. J. Biomol. Screen., 15, 1116-1122.
20. Zhang, X.H.D. (2010b) Assessing the size of gene or RNAi effects in multifactor highthroughput experiments. Pharmacogenomics, 11, 199-213.
21. Zhang, X.H.D. (2011) Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-Scale RNAi Research. Cambridge University Press, New York.
22. Zhang, X.H.D. et al. (2007) The use of strictly standardized mean difference for hit selection in primary RNA interference high-throughput screening experiments. J. Biomol. Screen., 12, 497-509.
23. Zhang, X.H.D. et al. (2010) The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens. J. Biomol. Screen., 15, 1123-1131.
24. Zhao, W.Q. et al. (2010) Inhibition of calcineurin-mediated endocytosis and alphaamino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors prevents amyloid beta oligomer-induced synaptic disruption. J. Biol. Chem., 285, 7619-7632.
25. Zhou, H.L. et al. (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe, 4, 495-504.