title: Specificity in ROS signaling and transcript signatures.
abstract: CONCLUSIONS
  Reactive oxygen species (ROS), important signaling molecules in plants, are involved in developmental control and stress adaptation. ROS production can trigger broad transcriptional changes; however, it is not clear how specificity in transcriptional regulation is achieved.
  
  
  BACKGROUND
  A large collection of public transcriptome data from the model plant Arabidopsis thaliana is available for analysis. These data can be used for the analysis of biological processes that are associated with ROS signaling and for the identification of suitable transcriptional indicators. Several online tools, such as Genevestigator and Expression Angler, have simplified the task to analyze, interpret, and visualize this wealth of data.
  
  
  RESULTS
  The analysis of the exact transcriptional responses to ROS requires the production of specific ROS in distinct subcellular compartments with precise timing, which is experimentally difficult. Analyses are further complicated by the effect of ROS production in one subcellular location on the ROS accumulation in other compartments. In addition, even subtle differences in the method of ROS production or treatment can lead to significantly different outcomes when various stimuli are compared.
  
  
  CONCLUSIONS
  Due to the difficulty of inducing ROS production specifically with regard to ROS type, subcellular localization, and timing, we propose that the concept of a "ROS marker gene" should be re-evaluated. We suggest guidelines for the analysis of transcriptional data in ROS signaling. The use of "ROS signatures," which consist of a set of genes that together can show characteristic and indicative responses, should be preferred over the use of individual marker genes.
authors.affiliation: 1 Division of Plant Biology, Department of Biosciences, University of Helsinki , Helsinki, Finland .
authors.forename: Lauri
authors.initials: L
authors.lastname: Vaahtera
authors.forename: Mikael
authors.initials: M
authors.lastname: Brosché
authors.forename: Michael
authors.initials: M
authors.lastname: Wrzaczek
authors.forename: Jaakko
authors.initials: J
authors.lastname: Kangasjärvi
mesh_terms: D017360:Arabidopsis / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D008954:Models, Biological; D017382:Reactive Oxygen Species / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: D029681:Arabidopsis Proteins; D017382:Reactive Oxygen Species