Functional Genomics Study and Database for Tuberculosis

描述（由申请人提供）：将研究结核分枝杆菌的功能基因组学，并构建用于科学和临床应用的数据库。该项目代表了微生物学和基因组学的一项新奋进，在耐多药结核病日益成为公共卫生威胁和科学家正在寻找具有新作用机制的新药的时候非常重要。鉴于微阵列技术对基因组学的巨大影响，该数据库将存储在各种设计的实验条件下产生的微阵列基因表达数据，并提供基于表达和调控谱的基因功能注释。M.将获得满足实验标准的药物敏感和耐药的结核病临床分离株。将开发一个基于网络的SQL Server关系数据库，以实现功能基因组学数据库，通过基于网络的图形界面提供查询和分析能力。数据库中的每个基因将通过其表达特征、共调控基因和相关的调控途径或网络以及其临床意义（如果适当）进行注释。此外，该数据库将每个基因与主要的生物信息学和基因组学数据库链接，以生成综合检索报告。所有功能基因组学数据和分析将被置于公共领域。与其他联邦资助的资源中心协同工作，该数据库的目的是让其他研究人员存款微阵列数据，进行数据分析，并获得程序代码，使内部系统。在这个项目中，将进行一系列差异和协调的全基因组基因表达研究，以探索药物靶点，耐药性和生物学。重要的抗结核药物和有前途的新候选药物将使用药物激发基因表达研究进行评估，以诱导药物作用产生的药物特异性基因表达模式。细胞生物学将使用同步M。基于体外诱导的非复制持久性的结核病培养物，从而将鉴定周期依赖性基因和相关的调节机制，并将研究在从非复制状态转变为复制状态期间发生的伴随代谢重编程的基因表达。这些研究将揭示许多共调控基因家族，并允许基于与已知功能基因的共表达来推断未表征基因的功能。结合聚类分析，顺式调控元件上游的调节子，并使用转录因子数据库的搜索将解开基因调控网络，并使生物学途径的推断和发现新的药物靶点。鉴定出的重要调控基因将进行进一步分析，以使用敲除菌株确认其调控作用。部分耐药和细菌持久性，这是两个重要的临床情况下经常遇到的结核病，将使用功能基因组学研究进行分析。所提出的方法的潜在价值已被证明，并承认优于以前的技术。研究结果将促进结核病的分子生物学知识和有益于公共卫生管理。

DESCRIPTION (provided by applicant): The functional genomics of Mycobacterium tuberculosis will be studied and a database will be constructed for both scientific and clinical applications. Representing a new endeavor in microbiology and genomics, this project is important at this time when multidrug-resistant tuberculosis is increasingly a public-health threat and scientists are seeking new drugs with novel mechanisms of action. In light of the tremendous impact of the microarray technology on genomics, the database will store the microarray gene expression data engendered under various designed experimental conditions as well as provides functional annotations of genes based on expression and regulation profiling. M. tuberculosis clinical isolates both drug-sensitive and -resistant that meet experimental criteria will be obtained. A web-based SQL Server relational database will be developed to implement the functional genomics database, providing query and analysis capabilities via a web-based graphical interface. Each gene in the database will be annotated by its expression characteristics, co-regulated genes and associated regulated pathways or networks, and its clinical significance, if appropriate. Furthermore, the database links each gene to major bioinformatics and genomics databases to produce an integrated retrieved report. All functional genomics data and analyses will be placed in the public domain. Working synergistically with other federally funded resource centers, the database is designed to allow other researchers to deposit microarray data, conduct data analysis, and obtain program code for making in-house systems. In this project, a set of differential and coordinated genome-wide gene expression studies will be performed to explore drug targets, drug resistance, and biology. Important anti-tubercular drugs and promising new drug candidates will be assessed using drug-challenged gene expression studies to induce drug-specific gene-expression patterns resulting from drug action. Cell biology will be investigated using synchronized M. tuberculosis culture based on in vitro induced non-replicating persistence so that cycle-dependent genes and pertinent regulatory mechanisms will be identified and gene expression accompanying metabolic reprogramming that occurs during shift from non-replicating to replicating states will be studied. These studies will uncover many co-regulated families of genes and allow the functions of uncharacterized genes to be deduced based on co-expression with genes of known function. Combining cluster analysis, search of cis-regulatory elements upstream of regulons, and use of transcription factor databases will unravel gene regulatory networks and enable inferences about biological pathways and discovery of novel drug targets. Important regulatory genes identified will be subjected to further analysis for confirming their regulatory roles using knockout strains. Partial drug resistance and bacterial persistence, which are two important clinical circumstances often encountered in tuberculosis, will be analyzed using functional-genomics studies. The potential value of the proposed methods has been demonstrated and advantages over previous technology been recognized. Research results will advance molecular biological knowledge and benefit public health management in tuberculosis.