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Gene Set Enrichment Analysis

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Protein Networks and Pathway Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 563))

Abstract

Set enrichment analytical methods have become commonplace tools applied to the analysis and interpretation of biological data. The statistical techniques are used to identify categorical biases within lists of genes, proteins, or metabolites. The goal is to discover the shared functions or properties of the biological items represented within the lists. Application of these methods can provide great biological insight, including the discovery of participation in the same biological activity or pathway, shared interacting genes or regulators, common cellular compartmentalization, or association with disease. The methods require ordered or unordered lists of biological items as input, understanding of the reference set from which the lists were selected, categorical classifiers describing the items, and a statistical algorithm to assess bias of each classifier. Due to the complexity of most algorithms and the number of calculations performed, computer software is almost always used for execution of the algorithm, as well as for presentation of the results.

This chapter will provide an overview of the statistical methods used to perform an enrichment analysis. Guidelines for assembly of the requisite information will be presented, with a focus on careful definition of the sets used by the statistical algorithms. The need for multiple test correction when working with large libraries of classifiers is emphasized, and we outline several options for performing the corrections. Finally, interpreting the results of such analysis will be discussed along with examples of recent research utilizing the techniques.

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Acknowledgments

We would like to thank Roumyana Yordanova for her thoughts and advice on statistical matters.

Author information

Authors and Affiliations

  1. Research & Development, Bristol-Myers Squibb Company, Pennington, NJ, USA

    Charles A. Tilford & Nathan O. Siemers

Authors
  1. Charles A. Tilford
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  2. Nathan O. Siemers
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Editor information

Editors and Affiliations

  1. GeneGo Inc., Saxony Road 169, Encinitas, 92024, U.S.A.

    Yuri Nikolsky

  2. GeneGo Inc., Saxony Road 169, Encinitas, 92024, U.S.A.

    Julie Bryant

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Tilford, C.A., Siemers, N.O. (2009). Gene Set Enrichment Analysis. In: Nikolsky, Y., Bryant, J. (eds) Protein Networks and Pathway Analysis. Methods in Molecular Biology, vol 563. Humana Press. https://doi.org/10.1007/978-1-60761-175-2_6

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  • DOI: https://doi.org/10.1007/978-1-60761-175-2_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-174-5

  • Online ISBN: 978-1-60761-175-2

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