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Cell Perturbation Screens for Target Identification by RNAi

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Bioinformatics and Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 910))

Abstract

Over the last decade, cell-based screening has become a powerful method in target identification and plays an important role both in basic research and drug discovery. The availability of whole genome sequences and improvements in cell-based screening techniques opened new avenues for high-throughput experiments. Large libraries of RNA interference reagents available for many organisms allow the dissection of broad spectrum of cellular processes. Here, we describe the current state of the large-scale phenotype screening with a focus on cell-based screens. We underline the importance and provide details of screen design, scalability, performance, data analysis, and hit prioritization. Similar to classical high-throughput in vitro screens with defined-target approaches in the past, cell-based screens depend on a successful establishment of robust phenotypic assays, the ability to quantitatively measure phenotypic changes and bioinformatics methods for data analysis, integration, and interpretation.

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Acknowledgements

The authors would like to thank Julia Gross and Thomas Sandmann for critical comments on the manuscript. This work has been in part supported by NGFN-Plus NeuroNet.

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Authors and Affiliations

  1. Division of Signaling and Functional Genomics, Department for Cell and Molecular Biology, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany

    Kubilay Demir & Michael Boutros

Authors
  1. Kubilay Demir
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  2. Michael Boutros
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Corresponding author

Correspondence to Michael Boutros .

Editor information

Editors and Affiliations

  1. , Department of Pathology, The University of New Mexico, Camino de Salud 915, Albuquerque, 87131, New Mexico, USA

    Richard S. Larson

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Demir, K., Boutros, M. (2012). Cell Perturbation Screens for Target Identification by RNAi. In: Larson, R. (eds) Bioinformatics and Drug Discovery. Methods in Molecular Biology, vol 910. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-965-5_1

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  • DOI: https://doi.org/10.1007/978-1-61779-965-5_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-964-8

  • Online ISBN: 978-1-61779-965-5

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