A portal and integrative collaborative analysis platform for GTEx

GTEx 的门户和综合协作分析平台

• 批准号: 10181004
• 负责人: KRISTIN ARDLIE
• 金额: $ 63.59万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10181004
• 关键词: Address; Back; Benchmarking; Biological Assay; ChIP-seq; Communities; Complex; Computer software; DNA Methylation; Data; Data Analyses; Data Set; Data Sources; Deoxyribonuclease I; Development; Disease; Docking; Documentation; Educational workshop; Feedback; Focus Groups; Gene Expression; Genetic Variation; Genomics; Genotype; Genotype-Tissue Expression Project; Growth; Human Biology; Hypersensitivity; Individual; Joints; Maintenance; Mass Spectrum Analysis; Methods; Molecular; Molecular Analysis; Molecular Profiling; Organ; Process; Production; Protein Methylation; Proteins; Quality Control; Quantitative Trait Loci; RNA Sequences; RNA Splicing; Research Personnel; Resources; Running; Sampling; Site; Source; Technology; Tissues; Training; Update; Visual; Visualization; Visualization software; Work; analysis pipeline; analytical method; base; cohort; data access; data exploration; data integration; data tools; data visualization; design; epigenome; exome; flexibility; genetic resource; genome wide association study; human tissue; improved; large datasets; member; miRNA expression profiling; multiple data types; novel; open source; outreach; repository; skills; tool; transcriptome sequencing; whole genome

Project Summary Abstract: Our capability to apply high-throughput molecular profiling technologies to increasingly large cohorts and sample sets is significantly expanding our understanding of human biology and complex disease. The Genotype Tissue-Expression (GTEx) project is creating a unique resource of genetic variation and gene expression across a wide range of human tissues. Upon completion this will include RNA sequence data from over 25,000 samples spanning 53 human tissues/organs and whole genome and exome sequence data from 960 donors. Additional data types not yet generated will include miRNA-seq, protein levels, DNA methylation, ChIP-seq, and DNase I hypersensitive site data among others. The ability to easily access, interpret and integrate these large data sets by a wide range of users with varying needs and skills is becoming of critical importance to leverage the full utility of the data. The GTEx Portal (http://gtexportal.org/) is the most widely accessed resource for the GTEx project, hosting all unprotected data, analysis results and numerous visual exploration tools, and has been enthusiastically received by the scientific community. To maximize the impact of this resource, we plan to expand the portal to: host data currently in production and new data types still to be generated; present novel and integrative analyses of existing data, and data from external sources; and to develop and share flexible tools for data analysis, visualization and access. Aim 1. We will host and support all open-access GTEx data and analysis results, performing systematic re-analyses of the data with new methods to reflect the state-of-the-art in RNA-seq analysis. We will add all new data sets to the portal to include novel assays (e.g. mi-RNA-seq, protein, methylation assays, etc/), derived analysis results (e.g. trans-eQTLs, splice- QTLs, GWAS enrichment analyses, protein-QTLs, etc.), and RNA-seq data sets from external investigators. Aim 2. We will work closely with both small focus groups of tool developers and engage our large user-base to identify and prioritize new features for development to display and integrate between multiple data types, and collaborate with other large genomic resources (e.g. ENCODE, UCSC and ENSEMBL browsers) to enable better integration of data sources and to enhance the utility and accessibility of the GTEx resource. Aim 3. We will automate and share all analysis pipeline tools with the scientific community. To support a wide range of user access needs, we will develop an open-source API to provide comprehensive data access, and also improve visualization tools and user-driven data analyses on the portal. To maximize use of the resource, we will design and offer training videos and outreach workshops.

项目摘要摘要： 我们将高通量分子图谱技术应用于越来越大的队列和 样本集极大地扩展了我们对人类生物学和复杂疾病的理解。这个 基因组织表达(GTEx)计划正在创造一个独特的遗传变异和基因资源 在广泛的人体组织中表达。完成后，这将包括RNA序列数据 来自53个人类组织/器官以及全基因组和外显子组序列的超过25,000个样本 来自960名捐赠者的数据。尚未生成的其他数据类型将包括miRNA-seq、蛋白质水平、 DNA甲基化、芯片序列和DNase I超敏位点数据等。能够轻松地 由具有不同需求的广泛用户访问、解释和集成这些大型数据集 要充分利用数据的效用，技能正变得至关重要。GTEx门户网站 (http://gtexportal.org/)是GTEx项目访问最广泛的资源，托管所有 不受保护的数据、分析结果和无数可视化的探索工具，并得到了热情的 受到科学界的欢迎。为了最大限度地发挥这一资源的影响，我们计划扩大 门户：托管当前生产中的数据和仍待生成的新数据类型；呈现新颖和 对现有数据和来自外部来源的数据进行综合分析；并灵活开发和共享 用于数据分析、可视化和访问的工具。目标1.我们将托管并支持所有开放访问的GTEx 数据和分析结果，用新的方法对数据进行系统的重新分析，以反映 最先进的rna-seq分析技术。我们将向门户添加所有新的数据集，以包括新的分析 (例如，mi-RNA-seq、蛋白质、甲基化分析等)，导出的分析结果(例如，反式eQTL、剪接- QTL、Gwas富集度分析、蛋白质QTL等)，以及来自外部的RNA-SEQ数据集 调查人员。目标2.我们将与工具开发人员的小型重点小组和参与 我们庞大的用户群，可识别并确定要开发的新功能的优先顺序，以显示和集成 在多种数据类型之间，并与其他大型基因组资源(例如ENCODE、UCSC)协作 和EnSembl浏览器)以实现更好的数据源集成，并增强实用程序和 GTEx资源的可访问性。目标3.我们将自动化所有分析管道工具并与其共享 科学界。为了支持广泛的用户访问需求，我们将开发一个开源的 API提供全面的数据访问，并改进可视化工具和用户驱动的数据 门户网站上的分析。为了最大限度地利用资源，我们将设计和提供培训视频和 外展讲习班。