title: Genomewide effects of peroxisome proliferator-activated receptor gamma in macrophages and dendritic cells--revealing complexity through systems biology.
abstract: BACKGROUND
  Systems biology approaches have become indispensable tools in biomedical and basic research. These data integrating bioinformatic methods gained prominence after high-throughput technologies became available to investigate complex cellular processes, such as transcriptional regulation and protein-protein interactions, on a scale that had not been studied before. Immunology is one of the medical fields that systems biology impacted profoundly due to the plasticity of cell types involved and the accessibility of a wide range of experimental models.
  
  
  METHODS
  In this review, we summarize the most important recent genomewide studies exploring the function of peroxisome proliferator-activated receptor γ in macrophages and dendritic cells. PPARγ ChIP-seq experiments were performed in adipocytes derived from embryonic stem cells to complement the existing data sets and to provide comparators to macrophage data. Finally, lists of regulated genes generated from such experiments were analysed with bioinformatics and system biology approaches.
  
  
  RESULTS
  We show that genomewide studies utilizing high-throughput data acquisition methods made it possible to gain deeper insights into the role of PPARγ in these immune cell types. We also demonstrate that analysis and visualization of data using network-based approaches can be used to identify novel genes and functions regulated by the receptor.
  
  
  CONCLUSIONS
  The example of PPARγ in macrophages and dendritic cells highlights the crucial importance of systems biology approaches in establishing novel cellular functions for long-known signaling pathways.
authors.affiliation: Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary.
authors.forename: Ixchelt
authors.initials: I
authors.lastname: Cuaranta-Monroy
authors.affiliation: Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary.
authors.forename: Mate
authors.initials: M
authors.lastname: Kiss
authors.affiliation: Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Simandi
authors.affiliation: Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary.|Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.|MTA-DE 'Lendulet' Immunogenomics Research Group, Debrecen, Hungary.
authors.forename: Laszlo
authors.initials: L
authors.lastname: Nagy
mesh_terms: D017667:Adipocytes / Q000276:immunology; D003713:Dendritic Cells / Q000276:immunology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008264:Macrophages / Q000276:immunology*; D047495:PPAR gamma / Q000235:genetics / Q000276:immunology*; D015398:Signal Transduction; D049490:Systems Biology
chemical_list: D047495:PPAR gamma
keywords: Dendritic cells; genomewide studies; macrophage; nuclear receptor; peroxisome proliferator-activated receptor gamma; systems biology