A Comprehensive Resource for Escherichia coli Genomic Data and Tools

摘要 大肠杆菌是生物学中利用最多的单个细胞。它是生物技术革命的基石， 也是我们了解细菌分子和细胞生理学的主要模式生物。尽管 它的核心重要性是，没有一个单一的资源可以提供对不断增长的大肠杆菌基因组学的了解 数据。RegulonDB已经是了解大肠杆菌基因调控的主要门户。我们建议 在三个关键方面将RegulonDB扩展为一个急需的大肠杆菌基因组数据门户：(1)我们将 整理所有可用的大肠杆菌高通量基因组数据集，以一致的方式分析这些数据集， 并通过访问、查询、可视化和分析工具将数据集成到RegulonDB中。数据集 将包括第一份基于ChIP-Seq和RNA-Seq的全面的大肠杆菌调控网络图 目前由其中两个PI生成。(2)我们将使用比较基因组数据扩展RegulonDB 横跨肠杆菌科。这将包括所有主要的代表的基因组数据 肠杆菌科各属。它还将包括深度人工精选文献和基因组数据集 与大肠杆菌有关的三种主要病原体：肠沙门氏菌、肺炎克雷伯氏菌和鼠疫耶尔森氏菌。在……里面 此外，我们将在这三个序列中的一组保守的TF中执行第一个比较的CHIP-SEQ映射 种和大肠杆菌。这将提供第一个全面的观点，在大肠杆菌和 这些病原体基于保守的TF中结合位点的全面图谱。它还将提供一个 在这些和其他肠杆菌科物种中生成完整的调控图谱的框架。(3)我们会 提供细菌芯片序列分析的在线服务器。该服务器将专门针对独特的 细菌CHIP-SEQ的特点和缺陷。该服务器将使新一代微生物学家 获得了ChIPSeq的功能，用于全面绘制转录因子-DNA结合图。

ABSTRACT Escherichia coli is the single most utilized cell in biology. It is the cornerstone of the biotechnology revolution, and the principal model organism for our understanding of bacterial molecular and cellular physiology. Despite its central importance, there is no single resource providing access to the growing body of E. coli genomics data. RegulonDB is already the primary portal for curated knowledge of E. coli gene regulation. We propose to expand RegulonDB to be a critically needed portal for E. coli genomic data in three key ways: (1) We will curate all available E. coli highthroughput genomic data sets, analyze these data sets in a consistent fashion, and integrate the data into RegulonDB with tools for access, query, visualization, and analysis. The datasets will include the first comprehensive map of the E. coli regulatory network based on ChIP-Seq and RNA-seq currently being generated by two of the PIs. (2) We will extend RegulonDB with comparative genomic data spanning the Enterobacteriaceae. This will include genomic data for representatives of all major Enterobacteriaceae genera. It will also include deep manual curation of the literature and genomic data sets for three key pathogens related to E. coli: Salmonella enterica, Klebsiella pneumoniae, and Yersinia pestis. In addition, we will perform the first comparative ChIP-Seq mapping in a set of conserved TFs in these three species and E. coli. This will provide the first broad view of the evolution of regulation between E. coli and these pathogens based on the comprehensive mapping of binding sites in conserved TFs. It will also provide a framework for generating complete regulatory maps in these and other Enterobacteriaceae species. (3) We will provide an online server for bacterial ChIP-Seq analysis. The server will be specifically tailored to the unique characteristics and pitfalls of ChIP-Seq in bacteria. The server will enable a new generation of microbiologists access to the power of ChIPSeq for the comprehensive mapping of transcription factor-DNA binding.