Integrated Standardized Express. Analytical Tools

描述（由申请人提供）：DNA数据库是科学的范式转变，其中大规模数据生成的最终结果不是那么多的出版物，而是具有具有高准确性和灵敏度的集成组件数据库的基于网络的公共资源（基因组浏览器）。基因组浏览器正在迅速成为生物医学研究界的主要工具之一，并大大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”，在这个意义上，有相对较少的变量要考虑;例如，“时间”和“幅度”通常不是变量。RNA和蛋白质的全基因组信息更具动态性，具有更多的变量，其中大多数是动态的。目前在RNA表达谱数据中提供公共访问数据库的努力在很大程度上局限于“数据库”，只有有限的查询工具和交叉实验研究可能。开发更强大的表达谱数据仓库和分析工具的一个主要限制是缺乏标准的实验平台，以及信号/噪声解释的相当大的困难。我们最近规避了许多这些限制，并公开了第一个Web-Oracle集成表达式分析数据库。我们已经开发了严格的QC/SOP协议，使用数据密集型和准确的Affytechnology平台，已经开发了一个网络查询数据仓库与一些分析工具，并编写和实施了自动化数据转换协议的网络发布到我们的网络服务器和NCBI GEO。事实上，流行的UCSC基因组浏览器中约50%的表达谱数据来自我们集成的内部/网络LIMS Oracle数据仓库（目前存储和分析了5，350次扫描）。在这里，我们的R21要求是开发创新的基于网络的分析工具，允许临时用户在我们的数据仓库中的任何或所有阵列中查询他们感兴趣的基因（人类，小鼠，大鼠; >140个项目，具有许多时间序列数据）。我们R21阶段的主要基准将是通过量化数据查询和用户反馈来展示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质量控制检查，将数据仓库扩展到超过10，000个脊椎动物档案，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.