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，进步和维护都需要 遵守和优化定义的过程，以确保创建基因组注释 现在和将来，与之相比 已经创建了。 Gencode资源也必须适应新技术 以及作为基因组发展领域的机会。一个主要目标 Gencode资源是确保质量控制（QC）和注释的数据验证。 Ensembl将将Gencode基因集与其他基因集（例如Uniprot）进行比较以检查 缺少基因或成绩单； 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进行手动验证 蛋白质组学数据。将通过维护良好的计算来确保项目稳定性 基础架构，足够的QC流程，可确保最高质量以及 通常以高价值格式发布免费的可用注释。注释策划 人和鼠标将完成，特别是现有的人类部分成绩单模型 将扩展到全长，扩展人类lncRNA注释，以及 完成鼠标注释的最初完整通行证的完成。 Gencode将合并个人 基因组表示和人口数据以可用的人类变异数据表示 序列水平（例如1000个基因组）和转录组水平（例如GTEX）和 由WTSI领导的小鼠基因组项目产生的16个小鼠菌株基因组。 来自个人和人群的数据将被注释。个人基因组资源将是 开发的，这将产生个人基因集的准确表示。两个飞行员 项目将有助于定义支持未来Gencode注释的最有效方法。 第一个试点项目将利用Gencode在发展人群参考基因组方面的经验 图形以试验基于人群的基因组的可扩展性且潜在的通用方法 注解。第二个试点项目将着重于将监管区域连接到监管 基因。 Gencode将增强基因的当前注释及其调节元件 因此注释取决于组织和细胞类型。对手动注释的需求 跨菌株和物种的成绩单可能超过Gencode提供此类此类的能力 通过现有机制提供服务，因此可以提交带注释的系统 数据将开发。所述的措施将确保2020年的Gencode是 对于基因组学的研究和临床应用，比今天更有价值。