MAPMAN:: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
MAPMAN:: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
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DOI：
10.1111/j.1365-313x.2004.02016.x
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发表时间：
2004-03-01
期刊：
影响因子：
7.2
通讯作者：
Stitt, M
中科院分区：
文献类型：
--
作者：
Thimm, O;Bläsing, O;Stitt, M
MAPMAN是一个用户驱动的工具，它将大量数据集显示在代谢途径或其他过程的图表上。清道夫模块将测量到的参数分配给分层类别(形成的‘bin’、‘subBIN’)。第一个构建的TRANSCRIPTSCAVENGER将拟南芥Affymetrix 22K阵列上的基因分组到>；200层级类别中，提供中央代谢的细分(对于几个途径，一直到单一酶水平)，以及次生代谢和细胞过程的概述。METABOLITESCAVENGER将数百种代谢物分组为结构上相关的化合物的途径或组。IMAGEANNOTATOR模块使用这些分组来组织实验数据集并将其显示在用户选择的图表上。模块化结构允许用户编辑现有类别，添加新类别，并为其他类型的数据开发清道夫模块。MAPMAN被用来分析两组22K Affymetrix阵列，这两组阵列研究了拟南芥莲座对低糖的反应：一组研究了夜长6小时后的反应，另一组在夜间结束时比较了野生型Columbia-0(Col-0)和无淀粉PGM突变体(胞质磷酸葡萄糖变位酶)。两种治疗方法在性质上有相似的反应。许多涉及光合作用、营养获取、氨基酸、核苷酸、脂类和细胞壁合成、细胞壁修饰以及RNA和蛋白质合成的基因被抑制。诱导了许多与氨基酸、核苷酸、脂肪和细胞壁破裂有关的基因。海藻糖代谢基因表达的变化指向海藻糖-6-磷酸(Tre6P)作为饥饿信号的作用。编码受体激酶、转录因子、信号通路的组成部分、参与翻译后修饰和周转的蛋白质以及参与细胞分裂素、脱落酸(ABA)和乙烯的合成和感知的蛋白质的表达发生了广泛的变化，揭示了调控网络的大规模重新布线是对糖耗竭的早期反应。
MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.