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Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data

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Plant Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1629))

Abstract

A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves.

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Authors and Affiliations

  1. Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

    Chun-Ping Yu & Wen-Hsiung Li

Authors
  1. Chun-Ping Yu
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  2. Wen-Hsiung Li
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Corresponding author

Correspondence to Wen-Hsiung Li .

Editor information

Editors and Affiliations

  1. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Kerstin Kaufmann

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Bernd Mueller-Roeber

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Yu, CP., Li, WH. (2017). Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7125-1_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7124-4

  • Online ISBN: 978-1-4939-7125-1

  • eBook Packages: Springer Protocols

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