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Gene Regulatory Networks pp 303–321Cite as

Learning Differential Module Networks Across Multiple Experimental Conditions

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1883))

Abstract

Module network inference is a statistical method to reconstruct gene regulatory networks, which uses probabilistic graphical models to learn modules of coregulated genes and their upstream regulatory programs from genome-wide gene expression and other omics data. Here, we review the basic theory of module network inference, present protocols for common gene regulatory network reconstruction scenarios based on the Lemon-Tree software, and show, using human gene expression data, how the software can also be applied to learn differential module networks across multiple experimental conditions.

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Acknowledgements

PE and TM are supported by Roslin Institute Strategic Programme funding from the BBSRC [BB/P013732/1].

Author information

Authors and Affiliations

  1. Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK

    Pau Erola

  2. Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France

    Eric Bonnet

  3. Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK

    Tom Michoel

  4. Current Address: Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway

    Tom Michoel

Authors
  1. Pau Erola
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  2. Eric Bonnet
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  3. Tom Michoel
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Corresponding author

Correspondence to Tom Michoel .

Editor information

Editors and Affiliations

  1. School of Informatics, University of Edinburgh, Edinburgh, UK

    Guido Sanguinetti

  2. Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium

    Vân Anh Huynh-Thu

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Erola, P., Bonnet, E., Michoel, T. (2019). Learning Differential Module Networks Across Multiple Experimental Conditions. In: Sanguinetti, G., Huynh-Thu, V. (eds) Gene Regulatory Networks. Methods in Molecular Biology, vol 1883. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8882-2_13

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  • DOI: https://doi.org/10.1007/978-1-4939-8882-2_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8881-5

  • Online ISBN: 978-1-4939-8882-2

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