'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences
'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences
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DOI：
10.1093/database/bau030
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发表时间：
2014-04-10
影响因子：
5.8
通讯作者：
Hehl, Reinhard
中科院分区：
文献类型：
--
作者：
Bolivar, Julio C.;Machens, Fabian;Hehl, Reinhard
利用生物信息学，假定的顺式调控序列可以很容易地识别特定基因集启动子上的模式识别程序。预测的顺式序列的丰度是将这些序列与基因表达调控的可能功能联系起来的主要挑战。为了确定预测的顺式序列的可能功能，开发了一个名为“计算机表达分析”的新型网络工具，将提交的顺式序列与拟南芥的基因表达数据相关联。该网络工具识别了拟南螺旋藻基因在一个定义的启动子区域中包含的序列，并将这些基因的表达与微阵列数据进行比较。结果是这些基因最有可能对非生物和生物应激条件作出反应的层次结构。在测试web工具的性能时，将已知的顺式调控序列提交给“计算机表达分析”，从而正确识别相关的应力条件。当使用最近发现的一种新的启动子响应序列WT-box （CGACTTTT）时，“计算机表达分析”预测在其启动子中含有该序列的基因最有可能是葡萄孢杆菌诱导的。与这一预测一致的是，在转基因拟南芥中，在灰绿杆菌中观察到在启动子中含有该序列的报告基因的最强诱导。
Using bioinformatics, putative cis-regulatory sequences can be easily identified using pattern recognition programs on promoters of specific gene sets. The abundance of predicted cis-sequences is a major challenge to associate these sequences with a possible function in gene expression regulation. To identify a possible function of the predicted cis-sequences, a novel web tool designated 'in silico expression analysis' was developed that correlates submitted cis-sequences with gene expression data from Arabidopsis thaliana. The web tool identifies the A. thaliana genes harbouring the sequence in a defined promoter region and compares the expression of these genes with microarray data. The result is a hierarchy of abiotic and biotic stress conditions to which these genes are most likely responsive. When testing the performance of the web tool, known cis-regulatory sequences were submitted to the 'in silico expression analysis' resulting in the correct identification of the associated stress conditions. When using a recently identified novel elicitor-responsive sequence, a WT-box (CGACTTTT), the 'in silico expression analysis' predicts that genes harbouring this sequence in their promoter are most likely Botrytis cinerea induced. Consistent with this prediction, the strongest induction of a reporter gene harbouring this sequence in the promoter is observed with B. cinerea in transgenic A. thaliana.