Genome-wide screens for effective siRNAs through assessing the size of siRNA effects.

BMC Research Notes
Xiaohua Douglas Zhang

Abstract

RNA interference (RNAi) has been seen as a revolution in functional genomics and system biology. Genome-wide RNAi research relies on the development of RNAi high-throughput screening (HTS) assays. One of the most fundamental challenges in RNAi HTS is to glean biological significance from mounds of data, which relies on the development of effective analytic methods for selecting effective small interfering RNAs (siRNAs). Based on a recently proposed parameter, strictly standardized mean difference (SSMD), I propose an analytic method for genome-wide screens of effective siRNAs through assessing and testing the size of siRNA effects. Central to this method is the capability of SSMD in quantifying siRNA effects. This method has relied on normal approximation, which works only in the primary screens but not in the confirmatory screens. In this paper, I explore the non-central t-distribution property of SSMD estimates and use this property to extend the SSMD-based method so that it works effectively in either primary or confirmatory screens as well as in any HTS screens with or without replicates. The SSMD-based method maintains a balanced control of false positives and false negatives. The central interest in genome-wide RNAi resea...Continue Reading

References

Feb 9, 2006·Nature Biotechnology·Nathalie MaloRobert Nadon
Sep 19, 2006·Molecular and Cellular Neurosciences·Amy S EspesethDaria Hazuda
Jan 25, 2008·Journal of Biomolecular Screening·Namjin ChungBerta Strulovici
May 16, 2008·Journal of Biomolecular Screening·Xiaohua Douglas ZhangMarc Ferrer
Jun 24, 2008·Journal of Biomolecular Screening·Xiaohua Douglas Zhang

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Citations

Aug 1, 2009·Nature Methods·Amanda BirminghamCaroline E Shamu
Feb 19, 2009·Bioinformatics·Xiaohua Douglas Zhang, Joseph F Heyse
Jul 17, 2008·Nucleic Acids Research·Xiaohua Douglas ZhangAmy S Espeseth
Sep 27, 2013·BioMed Research International·Shaoli DasKarol Kozak
Jul 31, 2012·Experimental Diabetes Research·Chandrasekhar AkileshwariGeereddy Bhanuprakash Reddy
Jul 15, 2015·Methods : a Companion to Methods in Enzymology·Debasis Panda, Sara Cherry
Feb 13, 2009·Journal of Biomolecular Screening·Xiaohua Douglas ZhangMarc Ferrer
Nov 16, 2018·MSphere·Grant BeyleveldMegan L Shaw
Jan 3, 2020·International Journal of Oncology·Su-Yeon LeeKyung-Ah Lee
Oct 27, 2017·Immunology·Abdolamir LandiSylvia van Drunen Littel-van den Hurk

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Methods Mentioned

BETA
random draws

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