title: Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine.
abstract: BACKGROUND
  Whole genome transcriptomics analysis is a very powerful approach because it gives an overview of the activity of genes in certain cells or tissue types. However, biological interpretation of such results can be rather tedious. MapMan is a software tool that displays large datasets (e.g. gene expression data) onto diagrams of metabolic pathways or other processes and thus enables easier interpretation of results. The grapevine (Vitis vinifera) genome sequence has recently become available bringing a new dimension into associated research. Two microarray platforms were designed based on the TIGR Gene Index database and used in several physiological studies.
  
  
  RESULTS
  To enable easy and effective visualization of those and further experiments, annotation of Vitis vinifera Gene Index (VvGI version 5) to MapMan ontology was set up. Due to specificities of grape physiology, we have created new pictorial representations focusing on three selected pathways: carotenoid pathway, terpenoid pathway and phenylpropanoid pathway, the products of these pathways being important for wine aroma, flavour and colour, as well as plant defence against pathogens. This new tool was validated on Affymetrix microarrays data obtained during berry ripening and it allowed the discovery of new aspects in process regulation. We here also present results on transcriptional profiling of grape plantlets after exposal to the fungal pathogen Eutypa lata using Operon microarrays including visualization of results with MapMan. The data show that the genes induced in infected plants, encode pathogenesis related proteins and enzymes of the flavonoid metabolism, which are well known as being responsive to fungal infection.
  
  
  CONCLUSIONS
  The extension of MapMan ontology to grapevine together with the newly constructed pictorial representations for carotenoid, terpenoid and phenylpropanoid metabolism provide an alternative approach to the analysis of grapevine gene expression experiments performed with Affymetrix or Operon microarrays. MapMan was first validated on an already published dataset and later used to obtain an overview of transcriptional changes in a susceptible grapevine - Eutypa lata interaction at the time of symptoms development, where we showed that the responsive genes belong to families known to be involved in the plant defence towards fungal infection (PR-proteins, enzymes of the phenylpropanoid pathway).
authors: National Institute of Biology, Department of Biotechnology and Systems Biology, Vecna pot 111, 1000 Ljubljana, Slovenia. ana.rotter@nib.si
authors: Ana
authors: A
authors: Rotter
authors: Céline
authors: C
authors: Camps
authors: Marc
authors: M
authors: Lohse
authors: Christian
authors: C
authors: Kappel
authors: Stefania
authors: S
authors: Pilati
authors: Matjaz
authors: M
authors: Hren
authors: Mark
authors: M
authors: Stitt
authors: Pierre
authors: P
authors: Coutos-Thévenot
authors: Claudio
authors: C
authors: Moser
authors: Björn
authors: B
authors: Usadel
authors: Serge
authors: S
authors: Delrot
authors: Kristina
authors: K
authors: Gruden
mesh_terms: D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D054884:Host-Pathogen Interactions; D020411:Oligonucleotide Array Sequence Analysis; D018749:RNA, Plant / Q000235:genetics; D027843:Vitis / Q000235:genetics* / Q000382:microbiology; D013098:Xylariales
chemical_list: D018749:RNA, Plant