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Bioinformatic Assessment of Macrophage Activation by the Innate Immune System

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Innate Immune Activation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1714))

Abstract

Weighted gene co-expression network analysis (WGCNA) allows for the identification and characterization of cell type-specific gene modules in complex transcriptome datasets. Here, we use a microarray dataset of human macrophages comprising 29 conditions and 299 samples generated by differentiation of CD14+ monocytes into macrophages followed by in vitro stimulations to identify stimulation-specific gene modules. These gene modules can be used for experimental validation, as well as further bioinformatic analysis to determine key pathways or upstream transcription factors.

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Author information

Authors and Affiliations

  1. Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany

    Thomas Ulas, Joachim L. Schultze & Marc Beyer

  2. Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany

    Joachim L. Schultze

  3. Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative Diseases, Bonn, Germany

    Marc Beyer

Authors
  1. Thomas Ulas
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  2. Joachim L. Schultze
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  3. Marc Beyer
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Corresponding authors

Correspondence to Thomas Ulas or Marc Beyer .

Editor information

Editors and Affiliations

  1. Inflammation Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Dominic De Nardo

  2. Chemical Biology Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Christine M De Nardo

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Ulas, T., Schultze, J.L., Beyer, M. (2018). Bioinformatic Assessment of Macrophage Activation by the Innate Immune System. In: De Nardo, D., De Nardo, C. (eds) Innate Immune Activation. Methods in Molecular Biology, vol 1714. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7519-8_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7519-8_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7518-1

  • Online ISBN: 978-1-4939-7519-8

  • eBook Packages: Springer Protocols

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