Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
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DOI：
10.1186/gb-2007-8-1-r7
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Coruzzi GM
中科院分区：
文献类型：
--
作者：
Gutiérrez RA;Lejay LV;Dean A;Chiaromonte F;Shasha DE;Coruzzi GM
定性网络模型和全基因组表达数据定义了拟南芥中的碳/氮响应分子机器，并表明碳/氮代谢产物的调控发生在多个水平。碳（C）和氮（N）代谢产物可以调节拟南芥基因的表达。在这里，我们使用multinetwork微阵列数据分析，以确定在拟南芥根系统的C和N调控的分子网络。我们使用拟南芥全基因组Affyssin基因芯片，以探讨全球基因表达的反应，在植物短暂暴露于矩阵的C和N处理。我们使用ANOVA分析来定义所有检测到的基因的调控的定量模型。我们的研究结果表明，大约一半的拟南芥转录组的C，N或CN相互作用的调节。我们发现了碳和氮之间相互作用的充分证据，包括参与代谢途径，蛋白质降解和生长素信号传导的基因。为了提供细胞分子网络如何响应CN处理而调整的全局但详细的视图，我们构建了拟南芥代谢和调节分子网络的定性多网络模型，包括6，176个基因，1，459个代谢物和它们之间的230，900个相互作用。我们将CN基因调控的定量模型与多网络中的接线图相结合，并确定了生物模块中对C、N或CN处理作出反应的特定相互作用基因。我们的研究结果表明，CN调节发生在多个水平，包括潜在的microRNA转录后控制。我们的系统数据集的CN治疗的网络分析表明，CN传感是一种机制，协调全球和协调调节的特定组的分子机器在植物细胞。
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis and indicate that regulation by carbon/nitrogen metabolites occurs at multiple levels. Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multinetwork analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system. We used the Arabidopsis whole genome Affymetrix gene chip to explore global gene expression responses in plants exposed transiently to a matrix of C and N treatments. We used ANOVA analysis to define quantitative models of regulation for all detected genes. Our results suggest that about half of the Arabidopsis transcriptome is regulated by C, N or CN interactions. We found ample evidence for interactions between C and N that include genes involved in metabolic pathways, protein degradation and auxin signaling. To provide a global, yet detailed, view of how the cell molecular network is adjusted in response to the CN treatments, we constructed a qualitative multinetwork model of the Arabidopsis metabolic and regulatory molecular network, including 6,176 genes, 1,459 metabolites and 230,900 interactions among them. We integrated the quantitative models of CN gene regulation with the wiring diagram in the multinetwork, and identified specific interacting genes in biological modules that respond to C, N or CN treatments. Our results indicate that CN regulation occurs at multiple levels, including potential post-transcriptional control by microRNAs. The network analysis of our systematic dataset of CN treatments indicates that CN sensing is a mechanism that coordinates the global and coordinated regulation of specific sets of molecular machines in the plant cell.
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影响因子：
4.3
作者：
Corbesier, L;Lejeune, P;Bernier, G
通讯作者：
Bernier, G
影响因子：
7.4
作者：
Scheible, WR;Morcuende, R;Stitt, M
通讯作者：
Stitt, M
影响因子：
11.6
作者：
Wang, RC;Guegler, K;Crawford, NM
通讯作者：
Crawford, NM
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
64.8
作者：
Kepinski, S;Leyser, O
通讯作者：
Leyser, O