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HAT: A Novel Statistical Approach to Discover Functional Regions in the Genome

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Tiling Arrays

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1067))

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Abstract

Tiling arrays are useful for exploring local functions of regions of the genome in an unbiased fashion. The exact determination of those genomic regions based on tiling-array data, e.g., generated by means of hybridization with immunopreciptated DNA-fragments to the arrays is a challenge. Many different statistical methodologies have been developed to find biological relevant regions-of-interest (ROI) by using the quantitative signal intensity of each probe. We previously developed a method called Hypergeometric Analysis of Tiling arrays (HAT) for the analysis of tiling-array data, but it is developed such that it can also be used to study data derived by genome-wide deep sequencing approaches. Here we applied HAT to analyze two publicly available tiling-array data sets. After the detection of statistically significant ROI, these are often used in additional analysis for hypothesis testing. We therefore discuss, by using the results of the tiling-array experiment, pathway and motif analyses.

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Acknowledgment

We wish to thank Claudia Erpelinck-Verschueren for technical assistance in the preparation of the CEBPA C-terminal mutant samples.

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Authors and Affiliations

  1. Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands

    Erdogan Taskesen, Bas Wouters & Ruud Delwel

Authors
  1. Erdogan Taskesen
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  2. Bas Wouters
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  3. Ruud Delwel
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Editor information

Editors and Affiliations

  1. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Tin-Lap Lee

  2. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Alfred Chun Shui Luk

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Taskesen, E., Wouters, B., Delwel, R. (2013). HAT: A Novel Statistical Approach to Discover Functional Regions in the Genome. In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_9

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  • DOI: https://doi.org/10.1007/978-1-62703-607-8_9

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-606-1

  • Online ISBN: 978-1-62703-607-8

  • eBook Packages: Springer Protocols

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