Gene Regulation E.coli Database Intergrated Environment

描述(由申请人提供)：本申请的目的是 围绕数据库实施集成计算环境 在大肠杆菌中的转录调控。此数据库RegulonDB包含 从有关调控元件和操纵子的文献中收集的信息 组织，它们在基因组中的位置，以及实验证据支持 被引用了1000多篇Medline原创文献。该项目将 将数据库转化为分析转录组和基因组的有用工具 蛋白质组实验。目标1是收集有关生长条件和它们的 相关的信号代谢物，并扩展图形功能 系统。目标2在于实现数据库并将其与以下工具相结合 基因组调控分析，如序列检索、模式发现和 模式搜索，以及句法识别器，以检测多个潜在的 上游区域内的监管要素。AIM 3以以下项目为中心 会使用转录组实验中的一组基因作为输入，并产生 上游有关其操纵子组织的图形或表格信息 受影响的调控位点、基因的功能类别和调控因子。全 这些工具将集成灵活的导航路径，其中一个 查询是另一个查询的输入。目标4包括扩展和应用 一种处理异构型数据的贝叶斯聚类方法 基因调控和新陈代谢信息。大肠埃希氏菌是这里的模式 系统，但是，这种方法和工具原则上可以应用于 研究其他微生物，从而产生更有效的方法来制造 使用当前可用的大量知识来实现 更好地了解它们的生物学，以及潜在的机制 影响人类健康。

DESCRIPTION (provided by applicant): The purpose of this application is to implement an integrated computational environment around a database on transcriptional regulation in E. coli. This database, RegulonDB, contains information gathered from the literature on regulatory elements and operon organization, their location in the genome, and experimental evidence supported by more than 1000 Medline original literature references. The project would transform the database into a useful tool for analysis of transcriptome and proteome experiments. Aim 1 is to gather data on growth conditions and their associated signal metabolites, and to expand the graphic capabilities of the system. Aim 2 consists in implementing and coupling the database with tools for genomic regulatory analyses, such as sequence retrieval, pattern discovery and pattern search, as well as a syntactic recognizer to detect multiple potential regulatory elements within an upstream region. Aim 3 centers on programs which would use as input a set of genes from a transcriptome experiment, and generate graphical or tabular information about their operon organization, upstream regulatory sites, functional classes of genes, and regulators affected. All these tools would integrate a flexible navigation path where the output of one query is the input for another one. Aim 4 consists in expanding and applying a Bayesian clustering method designed to deal with the heterogeneous type of information of gene regulation and metabolism. E. coli is here the model system, however, this approach and tools can in principle be applied to the study of other microbial organisms, resulting in more efficient ways to make use of currently available massive amounts of knowledge for the purpose of a better understanding of their biology, and potentially of their mechanisms affecting human health.