Identification of brassinosteroid-related genes by means of transcript co-response analyses.
Identification of brassinosteroid-related genes by means of transcript co-response analyses.
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DOI：
10.1093/nar/gki566
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发表时间：
2005
影响因子：
14.9
通讯作者：
Müssig C
中科院分区：
文献类型：
--
作者：
Lisso J;Steinhauser D;Altmann T;Kopka J;Müssig C
综合系统生物学数据库（CSB.DB）被用来揭示油菜素类固醇（BR）相关基因的表达谱的基础上的共同响应分析。表现出转录水平的同时变化的基因是共同转录调控的候选者。在数据矩阵中结合许多不同的实验可以排除异常值和转录水平的条件变化。查询CSB.DB与BR信号传导组分BRI1和BAK1的转录共应答：nasc0271数据库中代表的9694个基因中的301个显示与两个基因的共应答。正如预期的那样，这些基因包括通路相关基因（例如72个BR诱导基因），因为BRI1和BAK1蛋白是BR应答所必需的。但转录共反应使分析比直接方法更进一步，因为BR相关的非BR反应基因被鉴定。深入了解网络和基因的功能背景，因为决定表达模式的因素反映在相关性。我们的研究结果表明，转录协同反应分析提供了一个宝贵的资源，以揭示共同的基因调控模式。CSB.DB中的不同数据矩阵允许检查特定的生物学问题。所有汇总表均可通过CSB.DB公开查阅。这项工作提供了一个使用CSB.DB资源的可能路线图。
The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources.
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