CSB.DB: a comprehensive systems-biology database
CSB.DB: a comprehensive systems-biology database
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DOI：
10.1093/bioinformatics/bth398
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发表时间：
2004-12-12
期刊：
影响因子：
5.8
通讯作者：
Kopka, J
中科院分区：
文献类型：
--
作者：
Steinhauser, D;Usadel, B;Kopka, J
开放获取的综合系统生物学数据库（CSB.DB）提供了与其他生化和生理学知识相关的基因表达数据的生物统计分析结果。该数据库平台的主要目的是提供工具，支持深入了解生命的复杂性金字塔，特别关注转录和代谢物分析实验数据的整合。CSB.DB的核心部分，我们在本应用笔记中描述的，是一组共同响应数据库，目前主要关注三种关键模式生物，大肠杆菌，酿酒酵母和拟南芥。CSB.DB可以方便地访问大规模共同反应分析的结果，这些结果目前完全基于公开可获得的转录文件概要。通过扫描在不断变化的转录水平之间的最佳协同反应，CSB.DB可以推断基因功能相互作用的假设。这些假设是新颖的，无法通过序列同源性分析获得。该数据库能够搜索在共同转录控制下的基因对和更大的基因单位。此外，统计工具提供给用户，允许验证和比较在当前可用的预先选择的数据集上执行的基因查询所发现的那些共同反应。
The open access comprehensive systems-biology database (CSB.DB) presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this applications note, is a set of co-response databases that currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The database enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition, statistical tools are offered to the user, which allow validation and comparison of those co-responses that were discovered by gene queries performed on the currently available set of pre-selectable datasets.