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Identification of Candidate Functional Elements in the Genome from ChIP-seq Data

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Promoter Associated RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1543))

Abstract

ChIP-seq datasets provide a wealth of information for the identification of candidate regulatory elements in the genome. For this potential to be fully realized, methods for evaluating data quality and for distinguishing reproducible signal from technical and biological noise are necessary. Here, the computational methods for addressing these challenges developed by the ENCODE Consortium are described and the key considerations for analyzing and interpreting ChIP-seq data are discussed.

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Acknowledgments

The author wishes to thank Anshul Kundaje, members of the Barbara Wold and Richard Myers labs and of the ENCODE Consortium for many helpful discussions, and Gilberto DeSalvo and Matthew D. Smalley for critical reading of the manuscript.

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Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, 47405, USA

    Georgi K. Marinov

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  1. Georgi K. Marinov
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Correspondence to Georgi K. Marinov .

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Editors and Affiliations

  1. Experimental Therapeutics Group, Institute of Oncology Research, Bellinzona, Switzerland

    Sara Napoli

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Marinov, G.K. (2017). Identification of Candidate Functional Elements in the Genome from ChIP-seq Data. In: Napoli, S. (eds) Promoter Associated RNA. Methods in Molecular Biology, vol 1543. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6716-2_2

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  • DOI: https://doi.org/10.1007/978-1-4939-6716-2_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6714-8

  • Online ISBN: 978-1-4939-6716-2

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