COMPARATIVE FUNCTIONAL GENOMICS CORE

比较功能基因组学核心

• 批准号: 8728959
• 负责人: Benjamin L King
• 金额: $ 30.9万
• 依托单位: MOUNT DESERT ISLAND BIOLOGICAL LAB
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8728959
• 关键词: Aging; Animal Model; Bioinformatics; Biological databases; Biology; Biomedical Research; Candidate Disease Gene; Centers of Research Excellence; Chemicals; Collaborations; Communication; Communities; Comparative Biology; Complement; DNA; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Development; Disease; Embryo; Ensure; Foundations; Funding; Future; Gene Expression; Genes; Goals; High-Throughput Nucleotide Sequencing; Human; Information Resources Management; Instruction; International; Maintenance; MicroRNAs; Modeling; Mus; National Institute of Environmental Health Sciences; Natural regeneration; Online Systems; Outcome; Participant; Pilot Projects; Play; Process; Publications; Publishing; RNA; Regenerative Medicine; Research; Research Project Grants; Resource Informatics; Resources; Running; Scientist; Services; Small RNA; Software Engineering; Somatic Mutation; Speed; Stem cells; System; Technology; Tissues; Toxicogenomics; Update; Work; Xenopus; Zebrafish; base; comparative; cyber infrastructure; data exchange; data management; data portal; design; embryonic stem cell; experience; functional genomics; gene function; genome database; induced pluripotent stem cell; information gathering; innovation; member; mouse genome; novel; programs; regenerative; research study; response; self-renewal; sound; stem cell biology; tissue repair; tool; web interface; Aging; Animal Model; Bioinformatics; Biological databases; Biology; Biomedical Research; Candidate Disease Gene; Centers of Research Excellence; Chemicals; Collaborations; Communication; Communities; Comparative Biology; Complement; DNA; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Development; Disease; Embryo; Ensure; Foundations; Funding; Future; Gene Expression; Genes; Goals; High-Throughput Nucleotide Sequencing; Human; Information Resources Management; Instruction; International; Maintenance; MicroRNAs; Modeling; Mus; National Institute of Environmental Health Sciences; Natural regeneration; Online Systems; Outcome; Participant; Pilot Projects; Play; Process; Publications; Publishing; RNA; Regenerative Medicine; Research; Research Project Grants; Resource Informatics; Resources; Running; Scientist; Services; Small RNA; Software Engineering; Somatic Mutation; Speed; Stem cells; System; Technology; Tissues; Toxicogenomics; Update; Work; Xenopus; Zebrafish; base; comparative; cyber infrastructure; data exchange; data management; data portal; design; embryonic stem cell; experience; functional genomics; gene function; genome database; induced pluripotent stem cell; information gathering; innovation; member; mouse genome; novel; programs; regenerative; research study; response; self-renewal; sound; stem cell biology; tissue repair; tool; web interface

PROJECT SUMMARY (See instructions): The Comparative Functional Genomics Core will support COBRE Project Leaders by providing essential data management and analysis services, and developing a new web-based resource that integrates gene function data from COBRE projects with published studies in several diverse models of regeneration and stem cell self-renewal. Projects utilize high-throughput sequencing technologies and the Core will provide specialized expertise to Project Leaders to effectively manage, analyze and interpret results. Highly experienced Core staff will provide analysis services in a collaborative fashion and feature analysis workflows that will be updated on an ongoing basis. Services include an innovative tool for the analysis of known and novel microRNAs, termed miRMiner, that Core staff developed with a collaborator. The Core will also leverage regional cyberinfrastructure to remotely run large computations on two large clusters and use a regional data center for backup data storage and exchange. In addition to these services, the Core will also construct a new database resource for Project Leaders that has the long-term goal of providing a systems level view of regenerative biology and stem cell self-renewal. The Comparative Models of Regeneration Database (RegenDB) will integrate COBRE gene function data with published studies selected by Project Leaders from a number of comparative models. Initially, RegenDB will feature RNA and miRNA expression data from zebrafish, AxolotI, Xenopus, Polypterus senegalus and mouse embryonic and induced pluripotent stem cells. Project Leaders will be able to quickly compare expression levels of candidate genes within and across experiments they choose using a web interface. Core staff are key participants in the Comparative Toxicogenomics Database that started as an MDIBL pilot project and has since grown into an international resource. The Core will apply this experience to develop RegenDB in a similar fashion and plan to make a public web interface that the scientific community can use to access published data. In summary, the Core provides complementary expertise in bioinformatic analysis and software engineering that Project Leaders need to accomplish their research goals.

项目摘要（请参阅说明）： 比较功能基因组学核心将通过提供基本的数据管理和分析服务，并开发一种基于Web的新资源来支持COBRE项目领导者，该资源将来自Cobre项目的基因功能数据与已发表的研究集成了基因功能数据，该研究是在几种不同的再生模型和干细胞自我更新模型中。项目利用高通量测序技术，核心将提供专业的专业知识，以有效地管理，分析和解释结果。经验丰富的核心员工将以协作的方式提供分析服务，并提供功能分析工作流，这些服务将持续更新。服务包括一种用于分析已知和新颖的MicroRNA的创新工具，该工具称为Mirminer，该工具是与合作者一起开发的核心员工。核心还将利用区域网络基础结构在两个大型群集上远程运行大型计算，并使用区域数据中心进行备份数据存储和交换。除这些服务外，核心还将为项目负责人构建一个新的数据库资源，其长期目标是提供再生生物学和干细胞自我更新的系统级别。再生数据库（RegendB）的比较模型将将COBRE基因功能数据与来自许多比较模型的项目负责人选择的已发表的研究集成。最初，RegendB将具有来自斑马鱼，Axoloti，Xenopus，senegalus和小鼠胚胎和诱导多能干细胞的RNA和miRNA表达数据。项目负责人将能够快速比较他们选择使用Web界面内和跨实验中候选基因的表达水平。核心人员是比较毒物学数据库的主要参与者，该数据库最初是MDIBL试点项目，此后已发展成为国际资源。核心将采用这种经验以类似的方式开发登记，并计划制作科学界可以用来访问已发布数据的公共网络界面。总而言之，核心在生物信息学分析和软件工程方面提供了互补的专业知识，项目领导者需要实现其研究目标。