CORE-- GENOMIC AND BIONFORMATICS SUPPORT

核心——基因组学和生物信息学支持

• 批准号: 6946588
• 负责人: TOWIA A. LIBERMANN
• 金额: $ 11.78万
• 依托单位: BETH ISRAEL DEACONESS MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-07-01 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6946588
• 关键词: Internet; bioinformatics; biomedical facility; functional /structural genomics; gene expression; genetic transcription; genome; molecular biology information system; statistics /biometry; vascular endothelium

The primary goal of Core C will be to provide access to transcriptional profiling technologies to examine differential mRNA expression in the scope of endothelial cell heterogeneity and to delineate the mechanisms underlying site-specific phenotypes studied by the individual projects. The main objectives of the core will be to consult and train on functional genomics and bioinformatics, to provide standardized methods for quality control and validation of microarray experiments, to offer experienced onsite staff to perform microarray experiments and to analyze the data, to implement, update, and develop bioinformatics and biostatistics software tools for microarray analysis and data mining, and to develop a standardized database and interactive research portal. The core will label the cRNA probes, hybridize microarrays as well as provide a comprehensive analysis of the microarray data using biostatistical and bioinformatics software tools. Data generated by the core will be uploaded to the Research Portal and incorporated into a database for further analysis and querying by the individual investigators for hypothesis generation. The Core will establish the Endothelial Cell Heterogeneity Research Portal (ECHRP) to provide web-accessible data entry, annotation, cataloging facilities and state-of-the-start bioinformatics analyses. In addition, the core will develop new bioinformatics tools for data analysis and integration of metadata with the aim to build and simulate biological pathways. This will enable researchers from all Projects to maximally utilize the expression data sets to determine functional dependencies among the known and unknown genes and direct further biological validation of these putative dependencies. This critical biological validation step is described in each of the respective Project proposals. The facility will use Affymetrix GeneChip arrays of murine and human expressed sequences. By providing these services as a core function, we aim to save time and money and to establish quality controls and standardized procedures and reagents, which will lead to standardized data sets that can be compared and shared by different investigators in the program. In addition, integration of data sets from the different projects may by itself generate new insights not visible in individual data sets. The core will facilitate to integrate the wealth of data generated by the individual projects beyond the data generated by the microarray experiments.

核心C的主要目标将是提供对转录图谱技术的访问，以在内皮细胞异质性的范围内检查不同的mRNA表达，并描述由个别项目研究的特定部位表型的潜在机制。核心的主要目标将是咨询和培训功能基因组学和生物信息学，为微阵列实验的质量控制和验证提供标准化方法，提供有经验的现场工作人员进行微阵列实验和分析数据，实施、更新和开发用于微阵列分析和数据挖掘的生物信息学和生物统计学软件工具，并开发标准化数据库和互动研究门户网站。该核心将标记cRNA探针，杂交微阵列，并使用生物统计和生物信息学软件工具提供对微阵列数据的全面分析。核心产生的数据将被上传到研究门户网站，并纳入数据库，供个别调查人员进一步分析和查询，以产生假设。核心将建立内皮细胞异质性研究门户(ECHRP)，以提供网上可访问的数据输入、注释、编目设施和最新的生物信息学分析。此外，该核心将开发新的生物信息学工具，用于数据分析和元数据的整合，目的是建立和模拟生物途径。这 将使所有项目的研究人员能够最大限度地利用表达数据集来确定已知和未知基因之间的功能依赖关系，并指导这些假定依赖关系的进一步生物学验证。这一关键的生物验证步骤在每个相应的项目建议书中都有描述。该设施将使用Affymetrix基因芯片阵列的小鼠和人类表达的序列。通过提供这些服务作为核心功能，我们的目标是节省时间和金钱，并建立质量控制和标准化的程序和试剂，这将导致标准化的数据集，可以由项目中的不同研究人员进行比较和共享。此外，来自不同项目的数据集的整合本身可能会产生在单个数据集中看不到的新见解。这个 CORE将促进整合单个项目产生的丰富数据，而不是微阵列实验产生的数据。