GENCODE Resource Informatics

GENCODE 资源信息学

• 批准号: 9980962
• 负责人: Paul Flicek
• 金额: $ 106.93万
• 依托单位: EUROPEAN MOLECULAR BIOLOGY LABORATORY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-04-01 至 2021-09-13
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9980962
• 关键词: Address; Adherence; Code; Consumption; Data; Diploidy; Ensure; Future; Gene Expression; Genes; Genome; Genomics; Genotype-Tissue Expression Project; Graph; Human; Individual; Infrastructure; Length; Maintenance; Manuals; Measures; Modeling; Mouse Strains; Mus; Nucleic Acid Regulatory Sequences; Pilot Projects; Population; Procedures; Process; Proteomics; Quality Control; Regulator Genes; Regulatory Element; Research; Resource Informatics; Resources; Services; Speed; System; Tissues; Transcript; Validation; Variant; cell type; clinical application; computer infrastructure; experience; genome annotation; genome resource; mouse genome; new technology; population based; reference genome; scale up; tool; transcriptomics

RESOURCE INFORMATICS – PROJECT SUMMARY The creation, advancement and maintenance of the GENCODE resource requires both adherence to and optimization of defined processes that ensure the genome annotation created now and in the future will always be of the same or better standard compared to what has already been created. The GENCODE resource must also be attuned to the new technologies and opportunities that arise as the field of genomics evolves. A primary objective of the GENCODE resource is to ensure quality control (QC) and data validation of annotations. Ensembl will compare the GENCODE gene set to other gene sets (e.g. UniProt) to check for missing genes or transcripts; CNIO will validate the coding genes; the CNIO/CNIC proteomics pipeline will validates the gene models; CNIO/CNIC will perform manual verification for QC of proteomics data. Project stability will be ensured through a well-maintained computational infrastructure, adequate QC processes that will ensure the highest possible quality, as well as regular releases of freely available annotation in high value formats. The annotation curation for human and mouse will be completed, in particular the existing human partial transcript models will be extended to full length, expanding the human lncRNA annotation, as well as the completion of the initial full pass of the mouse annotation. GENCODE will incorporate individual genome representation and population data represented by available human variation data at both the sequence level (e.g. 1000 Genomes) and at the transcriptomic level (e.g. GTEx), and by the 16 mouse strain genomes produced by the Mouse Genomes Project led by the WTSI. Data from individuals and populations will be annotated. A personal genome resource will be developed, which will produce an accurate representation of an individual's gene set. Two pilot projects will help to define the most effective way to support future GENCODE annotations. The first pilot project will use GENCODE's experience in developing population reference genome graphs to pilot a scalable and potentially universal approach to population based genome annotation. The second pilot project will focus on connecting regulatory regions to regulated genes. GENCODE will enhance the current annotation of genes with their regulatory elements so that the annotation is dependent on tissue and cell type. The demand for manual annotation of transcripts across strains and species may outstrip GENCODE's ability to provide such services via existing mechanisms, therefore a system to enable the submission of annotated data will be developed. The described measures will ensure that GENCODE in 2020 will be significantly more valuable for research and clinical applications in genomics than today.

资源信息学--项目摘要 GENCODE资源的创建、升级和维护既需要 遵守并优化已定义的流程，以确保创建基因组注释 与过去相比，现在和将来的标准永远是相同的或更好的 已经创建。GENCODE资源也必须与新技术相协调 以及随着基因组学领域的发展而出现的机会。该计划的主要目标 GENCODE资源是为了确保注解的质量控制(QC)和数据验证。 EnSembl将把GENCODE基因集与其他基因集(例如UniProt)进行比较，以检查 缺失基因或转录本；CNIO将验证编码基因；CNIO/CNIC蛋白质组学 管道将验证基因模型；CNIO/CNIC将对QC执行手动验证 蛋白质组学数据。将通过维护良好的计算来确保项目的稳定性 基础设施，充分的QC流程，以确保尽可能高的质量 定期发布高价值格式的免费批注。的注释精选 人类和小鼠将完成，特别是现有的人类部分转录模型 将扩展到完整长度，扩展人类lncRNA批注以及 完成鼠标批注的初始完整过程。GENCODE将把个人 由可用的人类变异数据表示的基因组表示和种群数据，请访问 序列水平(例如1000个基因组)和转录水平(例如GTEx)，以及 由WTSI领导的小鼠基因组计划产生的16个小鼠品系基因组。 来自个人和人口的数据将被注释。个人基因组资源将是 开发出来的，这将产生一个人的基因组的准确表示。两名飞行员 项目将有助于定义支持未来GENCODE注释的最有效方式。这个 第一个试点项目将利用GENCODE在开发种群参考基因组方面的经验 图试验一种可扩展且潜在通用的基于种群的基因组方法 注释。第二个试点将集中在将监管地区与被监管地区连接起来 基因。GENCODE将增强当前对基因及其调控元件的注释 因此，注释依赖于组织和细胞类型。对人工标注的需求 跨菌株和物种的转录本的能力可能超过GENCODE的能力 通过现有机制提供的服务，因此是一种能够提交带注释的 数据将被开发出来。所述措施将确保2020年的GENCODE将 对基因组学的研究和临床应用来说，比今天更有价值。