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Pooled ShRNA Screenings: Computational Analysis

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Pancreatic Cancer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 980))

Abstract

Genome-wide RNA interference screening has emerged as a powerful tool for functional genomic studies of disease-related phenotypes and the discovery of molecular therapeutic targets for human diseases. Commercial short hairpin RNA (shRNA) libraries are commonly used in this area, and state-of-the-art technologies including microarray and next-generation sequencing have emerged as powerful methods to analyze shRNA-triggered phenotypes. However, computational analysis of this complex data remains challenging due to noise and small sample size from such large-scaled experiments. In this chapter we discuss the pipelines and statistical methods of processing, quality assessment, and post-analysis for both microarray- and sequencing-based screening data.

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Author information

Authors and Affiliations

  1. Department of Biomedical Informatics, Columbia University, New York, NY, USA

    Jiyang Yu & Andrea Califano

  2. Joint Centers for Systems Biology, Columbia University, New York, NY, USA

    Jiyang Yu

  3. Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA

    Preeti Putcha & Jose M. Silva

  4. Department of Pathology, Columbia University Medical Center, New York, NY, USA

    Preeti Putcha & Jose M. Silva

  5. Institute for Cancer Genetics, Columbia University, New York, NY, USA

    Andrea Califano

Authors
  1. Jiyang Yu
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  2. Preeti Putcha
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  3. Andrea Califano
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  4. Jose M. Silva
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Corresponding author

Correspondence to Jose M. Silva .

Editor information

Editors and Affiliations

  1. , Irving Cancer Research Center, Columbia University, St. Nicholas Avenue 1130, New York, 10032, New York, USA

    Gloria H. Su

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Yu, J., Putcha, P., Califano, A., Silva, J.M. (2013). Pooled ShRNA Screenings: Computational Analysis. In: Su, G. (eds) Pancreatic Cancer. Methods in Molecular Biology, vol 980. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-287-2_22

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  • DOI: https://doi.org/10.1007/978-1-62703-287-2_22

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-286-5

  • Online ISBN: 978-1-62703-287-2

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