Arabidopsis 2010: Constructing and Analyzing a Model Gene Regulatory Network

生物过程是由一系列复杂且相互关联的调控事件控制的，这些事件决定了个体基因能够在何时何地发挥作用。 生物学目前面临的一个挑战是将基因组织成网络，以准确描述它们的调控关系。在这个项目中，一个系统为基础的方法被用来构建和分析一个相对简单的基因网络，控制根表皮细胞分化的拟南芥。 一个细胞特异性的转录本分析方法已被用来定义一组根表皮基因，这些被组装成一个概率网络，通过系统地扰动特定的基因（节点）和定义独立的关系，从基因表达数据，使用贝叶斯网络分析。 这个网络将通过解决网络的不确定部分和通过使用分子，遗传和生化实验探测特定关系来完善和测试。 该项目有望为拟南芥基因网络的构建提供新的计算和实验工具，并揭示植物基因网络结构和电路的基本特征。 这些数据和生物资源将可从拟南芥生物资源中心，拟南芥信息资源（TAIR），和基因表达Omnibus.Broader影响：研究将提供一个异常丰富的跨学科培训经验的本科生，研究生，博士后研究员，它将有助于高中生的暑期研究计划。 该项目的研究将被纳入一个基于案例研究的生物技术课程的本科生和研究生。 从长远来看，该项目有望提高我们对植物基因调控机制的理解，并使生物和合成网络的合理设计用于植物改良。

Biological processes are controlled by sets of complex and interrelated regulatory events that determine when and where individual genes are able to act. A current challenge in biology is to organize genes into networks that accurately depict their regulatory relationships. In this project, a systems-based approach is being used to construct and analyze a relatively simple gene network that controls root epidermal cell differentiation in Arabidopsis. A cell-specific transcript profiling method has been used to define a set of root epidermis genes, and these are being assembled into a probabilistic network by systematically perturbing specific genes (nodes) and defining independence relationships from gene expression data using Bayesian network analysis. This network will be refined and tested by resolving uncertain parts of the network and by probing specific relationships using molecular, genetic, and biochemical experiments. The project is expected to provide new computational and experimental tools for gene network construction in Arabidopsis and to uncover fundamental features of plant gene network structure and circuitry. These data and biological resources will be accessible from the Arabidopsis Biological Resource Center, The Arabidopsis Information Resource (TAIR), and the Gene Expression Omnibus.Broader Impacts: The research will provide an unusually rich interdisciplinary training experience for undergraduates, graduate students, and postdoctoral fellows, and it will contribute to a summer research program for high school students. The project research will be incorporated into a case-study based biotechnology course for undergraduate and graduate students. In the long term, this project is expected to improve our understanding of plant gene regulatory mechanisms and enable the rational design of biological and synthetic networks for plant improvement.