Arthritis Genomics and Bioinformatics

关节炎基因组学和生物信息学

• 批准号: 7137074
• 负责人: CHRISTOPHE O. BENOIST
• 金额: $ 25.71万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7137074
• 关键词: Internet; bioinformatics; biomedical facility; biotechnology; cellular pathology; computer data analysis; computer program /software; functional /structural genomics; gene expression; information retrieval; joint disorder; meta analysis; microarray technology; molecular pathology; rheumatoid arthritis; synovitis

The overall goal of the Arthritis Genomics and Bioinformatics Core will be to support investigators in the Program utilizing microarray techniques. The core will provide uniform sample preparation, microarray design, data storage and bioinformatics, thus maximizing the reliability and compatibility of information obtained across the Program. The Core will perform standardized RNA preparation from joint tissues of experimental animals, and the amplification steps to generate labeled probe from small amounts of in vivo or in vitro derived RNA. This should help to generate highly comparable datasets throughout the Program. In addition, the Core will design a study-specific "Arthritis Chip", with spotted oligonucleotides that represent genes that vary during arthritogenesis. These custom chips will provide flexibility, allow a greater throughput than would be economically feasible with whole-genome chips, and again enhance data compatibility between the groups. The Core's bioinformatics personnel, which have acquired significant experience in microarray analysis, will guide, train, and help investigators through data analysis in an open and collaborative manner. The Core will provide access to basic analysis packages, and the ability to write custom software in a data-driven manner, in response to particular experimental situations. In addition, data analysis will benefit from a baseline of microarray data on gene expression during arthritis. A central server for secure data storage will house copies of the data, and Web-based software for data browsing will be applied as a Program-specific intranet and for public posting, as appropriate. In addition, the Core will perform data mining on the assembled data, explorations made possible by the coordinated processing and storage of the data, and by our pre-existing data on the evolution of gene expression in arthritic joints. Cross-experiment analyses will search for gene-gene correlations and clusters throughout a variety of conditions, and will generate functional gene hierarchies. These meta-analyses will enrich each of the individual analyses: defining, for example, the subset of genes that are still induced in spite of a genetic blockade of arthritis will help to pinpoint the cellular or functional level at which the gene is implicated. In addition, the meta-analyses made possible by the combined and coordinated datasets will also provide a unique insight into the "arthritis genome".

关节炎基因组学和生物信息学核心的总体目标是支持研究人员 利用微阵列技术的程序。核心将提供均匀的样品制备，微阵列 设计，数据存储和生物信息学，从而最大程度地提高信息的可靠性和兼容性 在整个程序中获得。核心将对关节组织进行标准化的RNA制备 实验动物以及从少量体内产生标记的探针的放大步骤 或体外衍生的RNA。这应该有助于在整个程序中生成高度可比的数据集。 此外，核心将设计一个特定研究的“关节炎芯片”，斑点是寡核苷酸 表示在关节生成期间变化的基因。这些自定义芯片将提供灵活性，允许更大 全基因组芯片在经济上可行的吞吐量，并再次增强数据 两组之间的兼容性。核心的生物信息学人员已经获得了重要的 微阵列分析的经验，将指导，培训和帮助调查人员通过数据分析开放 和协作方式。核心将提供对基本分析软件包的访问权限，并提供写作的能力 以数据驱动方式定制软件，以应对特定的实验情况。此外， 数据分析将受益于关节炎期间基因表达的微阵列数据基线。中央 用于安全数据存储的服务器将容纳数据的副本，并且基于Web的数据浏览软件将 可用作为特定于程序的内部网和用于公共发布。此外，核心将 对组装数据进行数据挖掘，通过协调处理进行探索 以及数据的存储，以及我们关于关节关节基因表达演化的进化的预先存在的数据。 跨体验分析将搜索各种各样的基因 - 基因相关性和簇 条件并将产生功能基因层次结构。这些荟萃分析将丰富 单个分析：例如，定义尽管有遗传的基因的子集 关节炎的封锁将有助于查明与基因有关的细胞或功能水平。在 此外，组合和协调数据集使荟萃分析可能还可以提供 对“关节炎基因组”的独特见解。