Data Management and Bioinformatics Core

数据管理和生物信息学核心

• 批准号: 10240685
• 负责人: ALAN A ADEREM
• 金额: $ 31.47万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10240685
• 关键词: ATAC-seq; Affect; Bioinformatics; Biological Response Modifiers; ChIP-seq; Collaborations; Collection; Communities; Computer Analysis; Data; Data Analyses; Data Set; Databases; Epigenetic Process; Ethylnitrosourea; Gene Expression; Gene Proteins; Genetic; Genomics; Goals; High-Throughput Nucleotide Sequencing; Immune; Immunity; Individual; Inflammation; Informatics; Infrastructure; Methods; Modeling; Modification; Mutant Strains Mice; Phenotype; Proteomics; Quality Control; Reagent; Research Personnel; Resources; Role; Signal Transduction; Structure; System; Systems Biology; Technology; Tissues; Update; Work; computerized tools; data management; epigenomics; genetic regulatory protein; high throughput technology; large datasets; large scale data; molecular phenotype; novel; phenotypic data; program dissemination; programs; transcriptome sequencing; transcriptomics; web portal; web site

Summary The Data Management and Bioinformatics Core (DMBC) will support each of the Projects and the overall goals of the program by applying multiple types of computational analyses to determine the functional role of novel immune regulators. This work will include: (i) processing and performing bioinformatics analysis of the large- scale data sets generated within the Projects and Cores; (ii) identifying genes, proteins, epigenetic modifications and tissue phenotypes that are most affected by immune perturbations; and (iii) by integrating internally generated and publicly available data sets to identify relevant co-expression modules and infer key regulators underlying immune phenotypes. Fully exploiting high throughput technologies such as RNA-seq, ChIP-seq and ATAC-seq, as well as multi-parameter molecular phenotyping (CyTOF, MIBI, CODEX) requires significant infrastructure and sophisticated analysis methods. The DMBC has deep expertise in the analysis of data generated by these technologies and has developed computational tools to discover novel immune regulators and determine their mechanisms of action. Furthermore, the DMBC has necessary resources to manage and analyze these large data sets and disseminate them to the program investigators and to the public via websites and existing public databases. The Core has developed a proven model for the informatics core in which individual computational investigators are imbedded within each of the projects. The advantage of this structure is that the computational biologists can participate at every level of the experimental program. The Core has found this structure to be particularly effective given the broad range of approaches used disparate at the various centers (systems biology, genetics, multi-parameter signaling analysis).

总结 数据管理和生物信息学核心（DMBC）将支持每个项目和总体目标 通过应用多种类型的计算分析来确定新的功能作用， 免疫调节剂这项工作将包括：（一）处理和进行生物信息学分析的大型- 在项目和核心内生成的规模数据集;（ii）识别基因、蛋白质、表观遗传 最受免疫扰动影响的修饰和组织表型;以及（iii）通过整合 内部生成的和公开可用的数据集，以鉴定相关的共表达模块并推断关键 免疫表型的调节因子。充分利用RNA-seq等高通量技术， ChIP-seq和ATAC-seq以及多参数分子表型分析（CyTOF、MIBI、CODEX）需要 重要的基础设施和复杂的分析方法。DMBC在以下方面拥有深厚的专业知识： 这些技术产生的数据，并开发了计算工具，以发现新的免疫 监管机构，并确定其作用机制。此外，DMBC拥有必要的资源， 管理和分析这些大型数据集，并将其分发给项目调查人员和 通过网站和现有的公共数据库公开。 核心已经为信息学核心开发了一个经过验证的模型， 每个项目中都有调查人员。这种结构的优点是， 计算生物学家可以参与实验计划的各个层面。内核发现了这个 考虑到各中心采用的方法各不相同， （系统生物学、遗传学、多参数信号分析）。