Rotter Ana, Camps Céline, Lohse Marc, Kappel Christian, Pilati Stefania, Hren Matjaz, Stitt Mark, Coutos-Thévenot Pierre, Moser Claudio, Usadel Björn, Delrot Serge, Gruden Kristina
National Institute of Biology, Department of Biotechnology and Systems Biology, Vecna pot 111, 1000 Ljubljana, Slovenia.
BMC Plant Biol. 2009 Aug 5;9:104. doi: 10.1186/1471-2229-9-104.
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.
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.
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).
全基因组转录组学分析是一种非常强大的方法，因为它能概述特定细胞或组织类型中基因的活性。然而，对这些结果进行生物学解释可能相当繁琐。MapMan是一种软件工具，可将大型数据集（如基因表达数据）显示在代谢途径或其他过程的图表上，从而使结果的解释更加容易。葡萄（葡萄属）基因组序列最近已公布，为相关研究带来了新的维度。基于TIGR基因索引数据库设计了两个微阵列平台，并用于多项生理学研究。
为了便于对这些实验及后续实验进行有效可视化，我们将葡萄属基因索引（VvGI版本5）注释到MapMan本体中。由于葡萄生理学的特殊性，我们创建了新的图形表示，重点关注三个选定的途径：类胡萝卜素途径、萜类化合物途径和苯丙烷类途径，这些途径的产物对葡萄酒的香气、风味和颜色以及植物对病原体的防御很重要。这个新工具在浆果成熟过程中获得的Affymetrix微阵列数据上得到了验证，并发现了过程调控中的新方面。我们还展示了使用Operon微阵列对葡萄幼苗暴露于真菌病原体葡萄座腔菌后的转录谱分析结果，包括用MapMan对结果进行可视化。数据表明，受感染植物中诱导的基因编码病程相关蛋白和类黄酮代谢酶，这些蛋白和酶对真菌感染有反应是众所周知的。
将MapMan本体扩展到葡萄属，以及新构建的类胡萝卜素、萜类化合物和苯丙烷类代谢的图形表示，为分析使用Affymetrix或Operon微阵列进行的葡萄属基因表达实验提供了另一种方法。MapMan首先在已发表的数据集上得到验证，随后用于在症状出现时获得易感葡萄 - 葡萄座腔菌相互作用中转录变化的概述，我们在其中表明，响应基因属于已知参与植物对真菌感染防御的家族（病程相关蛋白、苯丙烷类途径的酶）。
