Tech Development Core

技术开发核心

• 批准号: 10614629
• 负责人: RICHARD M BALDARELLI
• 金额: $ 41.37万
• 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/10614629
• 关键词: Anatomy; Biological; Biological Assay; Categories; Cell Lineage; Cells; Chickens; Complex; Consumption; Custom; Data; Data Set; Development; Developmental Anatomy; Disease; Ensure; Equilibrium; Expression Profiling; Fostering; Gene Expression Profiling; Genes; Genotype; Image; Immunohistochemistry; In Situ Hybridization; Internet; Intuition; Link; Maps; Metadata; Mus; Northern Blotting; Ontology; Pathway interactions; Pattern; Performance; Phenotype; Process; Productivity; Property; RNA; Rana; Resolution; Resources; Reverse Transcriptase Polymerase Chain Reaction; Sampling; Semantics; Site; Source; Specimen; System; Systems Biology; Text; Time; Tissues; Western Blotting; XenBase; Zebrafish; cell type; comparative; data integration; differential expression; embryo culture; experience; experimental study; gene expression database; gene function; gene product; improved; in vivo; indexing; mouse development; mutant; novel; protein protein interaction; sex; single-cell RNA sequencing; technology development; tool; transcriptome sequencing; web interface

Abstract - TECHNOLOGY DEVELOPMENT COMPONENT The Technology Development Component of the Gene Expression Database project (GXD) delivers to users the integrated expression data generated by Curation and Computation Components, via an intuitive and versatile web navigation paradigm. Users can refine their expression data searches in many ways (by properties of the mouse sample and/or by properties of the gene studied), and the summary of their search results has links to a variety of associated data (images, references, specimens, etc.). GXD provides an integrated combination of expression data from classical expression studies (RNA in situ hybridization and immunohistochemistry assays, northern blot, western blot and RT-PCR experiments) with high throughput RNA-Seq (HT) data, such that a user's search returns data from both classical and HT studies. This is a rare feature among expression resources, and it allows users to seamlessly exchange between these assay types, fostering comparison and confirmation. The Technology Development Component has four major parts (Aims) that can be sub-divided into interface components that deliver the following features: (1) Providing new ways to search and view expression results by mouse developmental anatomy. These include searches for genes expressed in tissues that follow differentiation paths and genes expressed in highly resolved cell types. (2) Adding new search and display functions for quantitative expression analyses, comparisons and profiling. This will give users ready access to gene sets that show altered expression patterns between defined sample states (between wild type and specific mutants, for example). (3) Providing graphical views of complex expression data, such as GXD's tissue x stage and tissue x gene matrices, and interactive RNA-Seq heat maps, to help users interpret expansive, integrated expression results. (4) Expanding the ability to analyze gene expression in the context of important biological concepts, such as gene function, phenotype and disease associations, and biological source parameters (like, tissue, stage and genotype), and adding a critical co-expression perspective to biological pathway and protein-protein interaction data by integrating with GXD data (genes must be co-expressed in the same cell, for their gene products to interact). (5) Enhancing users’ ability to compare expression between mouse and other important developmental species, such as zebra fish, frog and chicken. And lastly, (6) Allowing users to access GXD data for their own lists of genes and to use their GXD search results at other resources. All interface Aims proposed will be developed and administered with a balance of function and performance to ensure a productive GXD user experience.

摘要-技术开发部分 基因表达数据库项目（GXD）的技术开发组件向用户提供 由策展和计算组件生成的集成表达式数据，通过直观和 通用的网络导航范例。用户可以通过多种方式（通过 小鼠样品的性质和/或所研究的基因的性质），以及他们的搜索总结 结果链接到各种相关数据（图像、参考文献、标本等）。GXD提供了一个 整合来自经典表达研究的表达数据（RNA原位杂交， 免疫组织化学测定、北方印迹、蛋白质印迹和RT-PCR实验 RNA-Seq（HT）数据，使得用户的搜索返回来自经典和HT研究的数据。这是一个难得 特性，并且它允许用户在这些分析类型之间无缝交换， 促进比较和确认。技术开发部分有四个主要部分（目标） 可以细分为接口组件，提供以下功能：（1）提供新的方法， 通过小鼠发育解剖学搜索和查看表达结果。其中包括寻找基因 在遵循分化途径的组织中表达的基因和在高度分辨的细胞类型中表达的基因。（二） 添加新的搜索和显示功能，用于定量表达分析、比较和分析。这 将使用户可以随时访问基因集，这些基因集显示在定义的样本状态之间改变的表达模式 （例如，野生型和特定突变体之间）。(3)提供复杂表达式的图形视图 数据，如GXD的组织x阶段和组织x基因矩阵，以及交互式RNA-Seq热图，以帮助 用户解释扩展的、集成的表达式结果。(4)扩展分析基因表达的能力 在重要的生物学概念的背景下，如基因功能，表型和疾病关联， 和生物源参数（如组织、阶段和基因型），并添加关键的共表达 通过与GXD数据（基因）集成，对生物学途径和蛋白质-蛋白质相互作用数据进行透视 必须在同一细胞中共表达，以便它们的基因产物相互作用）。(5)提高用户的能力， 比较小鼠和其他重要发育物种如斑马鱼、青蛙和 鸡最后，（6）允许用户访问GXD数据，以获得他们自己的基因列表，并使用他们的GXD 搜索其他资源。所有提议的接口目标都将通过 平衡功能和性能，确保高效的GXD用户体验。