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A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes

机译:一种Gibbs采样方法来检测共表达基因上游区域中过度表达的基序

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摘要

AB - Microarray experiments can reveal important information about transcriptional regulation. In our case, we look for potential promoter regulatory elements in the upstream region of coexpressed genes. Here we present two modifications of the original Gibbs sampling algorithm for motif finding (Lawrence et al., 1993). First, we introduce the use of a probability distribution to estimate the number of copies of the motif in a sequence. Second, we describe the technical aspects of the incorporation of a higher-order background model whose application we discussed in Thijs et al. (2001). Our implementation is referred to as the Motif Sampler. We successfully validate our algorithm on several data sets. First, we show results for three sets of upstream sequences containing known motifs: 1) the G-box light-response element in plants, 2) elements involved in methionine response in Saccharomyces cerevisiae, and 3) the FNR O(2)-responsive element in bacteria. We use these data sets to explain the influence of the parameters on the performance of our algorithm. Second, we show results for upstream sequences from four clusters of coexpressed genes identified in a microarray experiment on wounding in Arabidopsis thaliana. Several motifs could be matched to regulatory elements from plant defence pathways in our database of plant cis-acting regulatory elements (PlantCARE). Some other strong motifs do not have corresponding motifs in PlantCARE but are promising candidates for further analysis
机译:AB-微阵列实验可以揭示有关转录调控的重要信息。在我们的案例中,我们在共表达基因的上游区域寻找潜在的启动子调控元件。在这里,我们提出了对原始Gibbs采样算法进行基序发现的两种改进(Lawrence等,1993)。首先,我们介绍使用概率分布来估计序列中基序副本的数量。其次,我们描述了结合高阶背景模型的技术方面,我们在Thijs等人中讨论了其应用。 (2001)。我们的实现称为Motif采样器。我们在多个数据集上成功验证了我们的算法。首先,我们显示了包含已知基序的三组上游序列的结果:1)植物中的G-box光响应元件,2)啤酒酵母中参与蛋氨酸响应的元件,以及3)FNR O(2)响应细菌中的元素。我们使用这些数据集来解释参数对算法性能的影响。其次,我们显示了在拟南芥创伤中的微阵列实验中鉴定出的共表达基因的四个簇的上游序列的结果。在我们的植物顺式作用调控元件数据库(PlantCARE)中,几种基序可以与植物防御途径的调控元件相匹配。其他一些强主题在PlantCARE中没有相应的主题,但有希望用于进一步分析

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