Development of a novel data mining tool to find cis-elements in rice gene promoter regions.
Development of a novel data mining tool to find cis-elements in rice gene promoter regions.
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DOI：
10.1186/1471-2229-8-20
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发表时间：
2008-02-27
影响因子：
5.3
通讯作者：
Kikuchi S
中科院分区：
文献类型：
--
作者：
Doi K;Hosaka A;Nagata T;Satoh K;Suzuki K;Mauleon R;Mendoza MJ;Bruskiewich R;Kikuchi S
超过35000个水稻全长cDNA的信息，加上在不同处理条件下收集的相关微阵列基因表达数据，使得识别在基因启动子中保守的、在不同条件下可能起关键作用的顺式调控元件成为可能。我们开发了一种新的工具，可以在差异调控基因的上游、下游或编码区搜索顺式元件候选。该工具首先通过基序搜索列出顺式元件候选，基于这样的假设：如果存在在给定的一组基因的调控中发挥重要作用的顺式元件，它们将在统计上被过度代表并将被保守。然后通过关联规则分析对列出的候选模体进行似然评分。这一策略依赖于这样一种想法，即在启动子区域过度表达的基序可以在这些基因的表达调控中发挥特定的作用。该工具的设计使任何生物研究人员都可以在可公开访问的互联网网站上轻松使用它。我们通过使用生长素诱导基因的数据集来评估该工具的准确性和实用性，这些基因具有经过充分研究的顺式元件。这项测试显示了该工具在识别顺式元件候选和相关基因集之间的显著关系方面的有效性。该工具列出了与感兴趣基因对应的可能的顺式元件基序，它将有助于更深入地了解植物的基因调控机制。
Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions. We have developed a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists cis-element candidates by motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site . We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied cis-elements. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes. The tool lists possible cis-element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.
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