A relational schema for both array-based and SAGE gene expression experiments.
A relational schema for both array-based and SAGE gene expression experiments.
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基于阵列和 SAGE 基因表达实验的关系模式。
DOI：
10.1093/bioinformatics/17.4.300
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发表时间：
2001
期刊：
影响因子：
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通讯作者：
Overton,GC
中科院分区：
文献类型：
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作者：
Stoeckert,C;Pizarro,A;Manduchi,E;Gibson,M;Brunk,B;Crabtree,J;Schug,J;Shen-Orr,S;Overton,GC
动机和结果：描述了一个关系模式， 捕获高度平行的基因表达实验， 不同的技术。这种模式源于建立一个 为从事不同生物系统研究的合作者提供的数据库 并在基因表达中使用不同类型的平台 实验以及不同类型的图像量化 软件这些表格在概念上分为三个部分 信息类别：平台，实验（其中包括 图像扫描和定量）和数据。的长处 模式是：（i）使用 基因索引;（ii）使用本体描述样本;（iii）减少 一个实验，一个单一的RNA来源的精确描述， 同时不丢失实验之间的关系 （四）保持原材料和原材料的一致性， 处理（例如清洗和规范化）数据并记录 数据被处理。其结果是一个新的模式，它可以容纳两者 数组和非数组数据，可扩展用于详细实验 描述是准确和一致的，并允许 实验之间基因的有意义的比较。可用性：该方案可在http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl.Contact获得：stoeckrt@pcbi.upenn.edu
Motivation and Results: A relational schema is described for capturing highly parallel gene expression experiments using different technologies. This schema grew out of efforts to build a database for collaborators working on different biological systems and using different types of platforms in their gene expression experiments as well as different types of image quantification software. The tables are conceptually organized into three categories of information: Platform, Experiment (which includes image scanning and quantification), and Data. The strengths of the schema are: (i) integrating information on array elements using a gene index; (ii) describing samples using ontologies; (iii) reducing an experiment to a single RNA source for precise descriptions yet not losing the relationships between experiments done at the same time or for the same project; and (iv) maintaining both raw and processed (e.g. cleansed and normalized) data and recording how the data is processed. The result is a novel schema, which can hold both array and non-array data, is extensible for detailed experimental descriptions that are precise and consistent, and allows for meaningful comparisons of genes between experiments.Availability: The schema is available at http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl.Contact: stoeckrt@pcbi.upenn.edu