Integrated Standardized Express. Analytical Tools

描述（由申请人提供）：DNA数据库是科学领域的一个范式转变，大规模数据生成的最终结果不是那么多的出版物，而是一个基于网络的公共资源（基因组浏览器），具有高精度和灵敏度的集成组件数据库。基因组浏览器正迅速成为生物医学研究界的主要工具之一，并极大地加快了遗传学和生物学的科学发现。DNA数据库是相对“静态”的，因为需要考虑的变量相对较少；如。“时间”和“振幅”通常不是变量。RNA和蛋白质的全基因组信息更加动态，有更多的变量，其中大多数本质上是动态的。目前在提供RNA表达谱数据的公共访问数据库方面的努力主要局限于“数据存储库”，只有有限的查询工具和交叉实验调查可能。开发更强大的表达剖面数据仓库和分析工具的主要限制是缺乏标准的实验平台，并且在信号/噪声解释方面相当困难。我们最近绕过了许多这些限制，并公开了第一个web-Oracle集成表达式分析数据库。我们使用数据密集型和精确的Affymetrix平台开发了严格的QC/SOP协议，使用一些分析工具开发了web查询数据仓库，并编写并实现了自动数据转换协议，用于web服务器和NCBI GEO的web发布。事实上，在流行的UCSC基因组浏览器中，大约50%的表达谱数据来自我们集成的内部/web LIMS Oracle数据仓库（目前存储和分析了5,350个扫描）。在这里，我们的R21要求是开发创新的基于web的分析工具，允许临时用户在我们的数据仓库（人类、小鼠、大鼠；bbb140项目，具有许多时间序列数据）中的任何或所有阵列中查询他们感兴趣的基因。我们的R21阶段的主要基准将是通过量化数据查询和用户反馈来证明这一创新工具的广泛普及。R33阶段将开发、实施远程数据输入和其他核心设施的QC检查，将仓库扩展到100万脊椎动物档案，并为网络数据仓库开发一套创新的用户分析和可视化工具。

DESCRIPTION (provided by applicant): The DNA databases have been a paradigm shift in science, where the end result of large-scale data generation is not so much publications, but rather a public web-based resource (genome browsers) with integrated component databases having high accuracy and sensitivity. The genome browsers are rapidly becoming one of the major tools of the bio-medical research community, and are dramatically expediting scientific discovery in genetics and biology in general. The DNA databases are relatively "static" in the sense that there are relatively few variables to be considered; e.g. "time", and "amplitude" are generally not variables. Genome-wide information on RNA and protein are much more dynamic, with many more variables, most of which are dynamic in nature. Current efforts at providing public access databases in RNA expression profile data have been largely limited to "data repositories", with only limited query tools and cross-experiment investigations possible. A major limitation of development of more powerful expression profile data warehouses and analytical tools has been the lack of a standard experimental platform, and considerable difficulty in signal/noise interpretation. We have recently circumvented many of these limitations, and have made public the first web-Oracle integrated expression-profiling database. We have developed strict QC/SOP protocols using the data-intensive and accurate Affymetrix platform, have developed a web-queried data warehouse with some analytical tools, and have written and implemented automated data conversion protocols for web publication to both our web server and NCBI GEO. Indeed, about 50% of all expression profile data in the popular UCSC genome browsers is from our integrated internal/web LIMS Oracle data warehouse (5,350 scans currently stored and analyzed). Here, our R21 request is to develop innovative web-based analytical tools that allow the casual user to query their gene of interest in any or all of the arrays in our data warehouse (human, mouse, rat; >140 projects, with many time series data). The major benchmark of our R21 phase will be the demonstration of widespread popularity of this innovative tool, by quantitation of data queries and user feedback. The R33 phase will develop, implementation of remote data entry and QC checks by other core facilities, expansion of the warehouse to > 10,000 vertebrate profiles, and development of a suite of innovative user analysis and visualization tools for the web data warehouse.