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Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors

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Computational Biology of Transcription Factor Binding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 674))

Abstract

Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data.

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Author information

Authors and Affiliations

  1. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Kenzie D. MacIsaac

  2. Molecular Profiling Research Informatics, Merck Research Laboratories, Boston, MA, USA

    Kenzie D. MacIsaac

  3. Computer Science and Artificial Intelligence Laboratory, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Ernest Fraenkel

Authors
  1. Kenzie D. MacIsaac
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  2. Ernest Fraenkel
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Correspondence to Kenzie D. MacIsaac .

Editor information

Editors and Affiliations

  1. , Department of Statistics, University of Nebraska-Lincoln, Vine Street 1901, Lincoln, 68588-0665, Nebraska, USA

    Istvan Ladunga

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MacIsaac, K.D., Fraenkel, E. (2010). Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors. In: Ladunga, I. (eds) Computational Biology of Transcription Factor Binding. Methods in Molecular Biology, vol 674. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-854-6_11

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  • DOI: https://doi.org/10.1007/978-1-60761-854-6_11

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-853-9

  • Online ISBN: 978-1-60761-854-6

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