Data Management and Bioinformatics Core

数据管理和生物信息学核心

基本信息

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
项目类别：
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

项目摘要

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).

概括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颖的功能角色免疫调节剂。这项工作将包括：（i）处理和执行大型生物信息学分析扩展项目和核心中生成的数据集； (ii) 识别基因、蛋白质、表观遗传受免疫扰动影响最大的修饰和组织表型； (iii) 通过整合内部生成和公开可用的数据集，用于识别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 在分析方面拥有深厚的专业知识这些技术生成的数据并开发了计算工具来发现新的免疫监管者并确定其行动机制。此外，DMBC 拥有必要的资源管理和分析这些大数据集并将其传播给项目研究人员和通过网站和现有公共数据库公开。该核心已经为信息学核心开发了一个经过验证的模型，其中单独的计算每个项目都有调查员参与。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级别。核心发现了这个鉴于各个中心使用的方法范围广泛、不同，该结构将特别有效（系统生物学、遗传学、多参数信号分析）。