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Bioinformatic Assessment of Macrophage Activation by the Innate Immune System

  • Thomas UlasEmail author
  • Joachim L. Schultze
  • Marc BeyerEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Keywords

Weighted gene co-expression network analysis Macrophages Transcriptome analysis Microarray RNA-seq Bioinformatics 

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Genomics & Immunoregulation, Life and Medical Sciences InstituteUniversity of BonnBonnGermany
  2. 2.Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of BonnBonnGermany
  3. 3.Molecular Immunology in Neurodegeneration, German Center for Neurodegenerative DiseasesBonnGermany

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