Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine.
Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine.
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DOI：
10.1186/1471-2229-9-104
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发表时间：
2009-08-05
影响因子：
5.3
通讯作者：
Gruden K
中科院分区：
文献类型：
--
作者：
Rotter A;Camps C;Lohse M;Kappel C;Pilati S;Hren M;Stitt M;Coutos-Thévenot P;Moser C;Usadel B;Delrot S;Gruden K
全基因组转录组学分析是一种非常强大的方法，因为它提供了某些细胞或组织类型中基因活性的概述。然而，对这些结果的生物学解释可能相当乏味。MapMan是一种软件工具，可以将大型数据集（例如基因表达数据）显示在代谢途径或其他过程的图表上，从而更容易解释结果。葡萄藤（葡萄属葡萄）基因组序列最近已成为可用的相关研究带来了新的层面。基于TIGR基因索引数据库设计了两个微阵列平台，并用于几项生理学研究。为了使这些和进一步的实验能够容易和有效地可视化，建立了葡萄属酿酒葡萄基因索引（VvGI版本5）到MapMan本体的注释。由于葡萄生理学的特殊性，我们创造了新的图形表示集中在三个选定的途径：类胡萝卜素途径，萜类途径和苯丙素途径，这些途径的产品是重要的葡萄酒香气，风味和颜色，以及植物防御病原体。这种新的工具在浆果成熟过程中获得的Affyphase微阵列数据上进行了验证，它允许发现过程调节的新方面。我们在这里还介绍了结果的葡萄试管苗的转录谱后，experienced到真菌病原体Eutypa lata使用操纵子微阵列，包括可视化的结果与MapMan。这些数据表明，在受感染的植物中诱导的基因编码与类黄酮代谢相关的致病性蛋白和酶，这些蛋白和酶被公知为响应于真菌感染。MapMan本体论的扩展葡萄与新构建的类胡萝卜素，萜类化合物和苯丙素代谢的图形表示一起提供了一种替代方法来分析葡萄藤基因表达实验与Affytron或操纵子微阵列。MapMan首先在一个已经发表的数据集上进行了验证，后来用于获得症状发展时易感葡萄藤Eutypa lata相互作用中转录变化的概述，其中我们表明响应基因属于已知参与植物防御真菌感染的家族（PR蛋白，苯丙素途径的酶）。
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).
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影响因子：
4.4
作者：
Deluc LG;Grimplet J;Wheatley MD;Tillett RL;Quilici DR;Osborne C;Schooley DA;Schlauch KA;Cushman JC;Cramer GR
通讯作者：
Cramer GR
影响因子：
--
作者：
Lardner, R;Stummer, BE;Scott, ES
通讯作者：
Scott, ES
影响因子：
7.4
作者：
Davies, C;Boss, PK;Robinson, SP
通讯作者：
Robinson, SP
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
DOI：
10.1111/j.1755-0238.1995.tb00086.x
发表时间：
1995-01-01
影响因子：
2.8
作者：
Coombe, B. G.
通讯作者：
Coombe, B. G.