Gene Expression Database for Mouse Development

小鼠发育基因表达数据库

• 批准号: 10413888
• 负责人: MARTIN RINGWALD
• 金额: $ 214.66万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-12-02 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10413888
• 关键词: Address; Adult; Anatomy; Animal Model; Applications Grants; Biological; Cells; Collaborations; Communities; Complex; Computer Analysis; Congenital Abnormality; Data; Data Set; Databases; Development; Disease; Documentation; Ensure; Feedback; Future; Gene Expression; Gene Expression Profile; Genetic; Goals; Health; Human; Human Development; Human Genetics; Image; Immunohistochemistry; In Situ; In Situ Hybridization; Informatics; Infrastructure; Knock-in; Knowledge; Laboratories; Literature; Maintenance; Malignant Neoplasms; Medical; Metadata; Modernization; Molecular; Molecular Analysis; Mouse Strains; Mus; Mutant Strains Mice; Northern Blotting; Ontology; Organism; Other Genetics; Pathway interactions; Pattern; Phenotype; Positioning Attribute; Process; Proteins; Public Health; Publications; RNA; Reporter; Research; Research Personnel; Resource Informatics; Resources; Reverse Transcriptase Polymerase Chain Reaction; Software Engineering; Tissues; Training; Triage; Western Blotting; Wild Type Mouse; Work; bioinformatics infrastructure; cell type; central database; complex data; data curation; editorial; experimental study; gene expression database; gene function; genetic information; improved; informatics infrastructure; mouse development; mouse genome; online tutorial; outreach; programs; single-cell RNA sequencing; software infrastructure; sound; tool; transcriptome sequencing

Abstract – OVERALL COMPONENT The goal of this application is the continued development and maintenance of the Gene Expression Database for Mouse Development (GXD). GXD is a well-established community resource. It integrates different types of expression data including biologically complex data, such as RNA in situ hybridization and immunohistochemistry results, and high-throughput expression data from RNA-seq experiments. It places these data in the larger biological context through integration with other Mouse Genome Informatics (MGI) resources and interconnections with many other databases, supporting complex queries that enable thorough biological and computational analyses. The specific aims of this proposal are (1) to continue and expand GXD’s curation of expression data and anatomical ontologies and ensure high-quality data annotation and integration. We will continue to curate data from RNA in situ hybridization, in situ-reporter knock-in, immunohistochemistry, RT-PCR, Northern blot and Western blot experiments; and expand our annotation of bulk and single-cell RNA-seq data sets. We will enhance the mouse anatomy ontology, and refine our expression annotations by combining anatomy and cell type terms. We will (2) maintain the GXD database and enhance GXD’s infrastructure and data entry interfaces to accommodate large volumes of expression data and to represent new types of data and relationships. We will enhance the database and software infrastructure to accommodate the expected increase in RNA-seq data. We will expand the database to represent anatomical differentiation pathways, as well as expression annotations to cell type terms. We will continue to modernize the editorial interface and expand the interface as needed for the annotation of new data types. We will automate more steps of the literature selection process to increase curation efficiency. We will (3) continue to evolve GXD’s user interface and develop advanced query and display tools. We will develop expression searches that allow the analysis of anatomical differentiation pathways and cell types. We will add support for quantitative expression analyses, comparisons and profiling. We will develop displays that superimpose expression data with molecular pathway and protein interaction data to support the analysis of molecular networks with co- expression information. We will (4) provide user support and promote use of GXD by the scientific community. We will continue to provide training and to solicit feedback on how we can improve GXD.

摘要 - 整体组件 该应用的目的是持续开发和维护基因表达 鼠标开发数据库（GXD）。 GXD是一个公认的社区资源。它整合 不同类型的表达数据，包括生物学上复杂的数据，例如RNA原位杂交和 免疫组织化学结果以及来自RNA-Seq实验的高通量表达数据。它位置 通过与其他小鼠基因组信息学（MGI）集成，在较大的生物环境中这些数据 资源和与许多其他数据库的互连，支持复杂的查询，这些查询可以彻底 生物学和计算分析。 该提案的具体目的是（1）继续并扩展GXD的表达数据和 解剖本体学并确保高质量的数据注释和集成。我们将继续 来自RNA原位杂交的策展数据，原位替代者敲入，免疫组织化学，RT-PCR，北部 印迹和蛋白质印迹实验；并扩展我们对批量和单细胞RNA-seq数据集的注释。我们 将增强小鼠解剖学本体，并通过结合解剖学和 细胞类型术语。我们将（2）维护GXD数据库并增强GXD的基础架构和数据输入 容纳大量表达数据并表示新类型的数据的接口和 关系。我们将增强数据库和软件基础架构，以适应预期的 RNA-seq数据增加。我们将扩展数据库以表示解剖学分化途径，如 以及对细胞类型项的表达注释。我们将继续现代化社论界面和 根据需要扩展接口，以注释新数据类型。我们将自动化更多的步骤 文献选择过程以提高策划效率。我们将（3）继续发展GXD的用户 接口并开发高级查询和显示工具。我们将开发允许的表达搜索 解剖学分化途径和细胞类型的分析。我们将增加对定量的支持 表达分析，比较和分析。我们将开发显示叠加表达数据的显示 使用分子途径和蛋白质相互作用数据，以支持与共同的分子网络分析 表达信息。我们将（4）提供用户支持并促进科学的GXD 社区。我们将继续提供培训，并征求有关如何改善GXD的反馈。