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The Use of Design Specificity in Standardized Mean Difference for Analysis of High throughput RNA Interference Screens

  • Conference paper
Book cover Information Technology in Bio- and Medical Informatics (ITBAM 2012)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 7451))

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Abstract

RNA interference (RNAi) high-content screening (HCS) enables massive parallel gene silencing and is increasingly being used to reveal novel connections between genes and disease-relevant phenotypes. The application of genome-scale RNAi relies on the development of high quality HCS assays. Strictly standardized mean difference (SSMD), introduced by Zhang et al. [1], provides a possibility for hit selection in HCS experiments. This method has relied on normal approximation, which works in the primary screens considering positive and negative controls. This paper describes a new extension of the SSMD, which integrates bioinformatics RNAi on-target analysis results for both the SSMD-based testing process and the use of SSMDas a ranking metric for hit selection by using additional controls generated from RNAi libraries.

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Author information

Authors and Affiliations

  1. LMSC, ETH Zurich, Switzerland

    Karol Kozak

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  1. Karol Kozak
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Ludwig-Maximilians-University, Oettingenstraße 67, 80538, München, Germany

    Christian Böhm

  2. Department of Computer Science, San Jose State University, One Washington Square, 95192-0249, San Jose, CA, USA

    Sami Khuri

  3. Faculty of Electrical Engineering, Department of Cybernetics, Czech Technical University, Technicka 2, 166 27, Prague 6, Czech Republic

    Lenka Lhotská

  4. Istituto di Informatica e Telematica del CNR, Via G. Moruzzi 1, 56124, Pisa, Italy

    M. Elena Renda

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© 2012 Springer-Verlag Berlin Heidelberg

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Kozak, K. (2012). The Use of Design Specificity in Standardized Mean Difference for Analysis of High throughput RNA Interference Screens. In: Böhm, C., Khuri, S., Lhotská, L., Renda, M.E. (eds) Information Technology in Bio- and Medical Informatics. ITBAM 2012. Lecture Notes in Computer Science, vol 7451. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32395-9_11

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  • DOI: https://doi.org/10.1007/978-3-642-32395-9_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-32394-2

  • Online ISBN: 978-3-642-32395-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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