Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
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DOI：
10.1093/bioinformatics/btg1038
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发表时间：
2003-07-01
期刊：
影响因子：
5.8
通讯作者：
Koller, D.
中科院分区：
文献类型：
--
作者：
Segal, E.;Yelensky, R.;Koller, D.
在本文中，我们描述了一种从基因表达和启动子序列数据来理解转录调控的方法。我们的目标是通过一个共同的基序概况来确定转录模块-在一组实验中共同调节的基因集。使用EM算法，我们的方法改进了模块分配和基序配置文件，以便最好地解释表达数据作为转录基序的函数。它还根据需要动态添加和删除基序，以提供表达数据的全基因组解释。我们在两个酿酒酵母基因表达数据集上对该方法进行了评估，结果表明，我们的方法在恢复已知基序和生成生物学上一致的模块方面优于标准方法。我们还将我们的结果与结合定位数据相结合，以获得与已知转录因子的调控关系，并表明许多推断关系在文献中得到支持。
In this paper, we describe an approach for understanding transcriptional regulation from both gene expression and promoter sequence data. We aim to identify transcriptional modules-sets of genes that are co-regulated in a set of experiments, through a common motif profile. Using the EM algorithm, our approach refines both the module assignment and the motif profile so as to best explain the expression data as a function of transcriptional motifs. It also dynamically adds and deletes motifs, as required to provide a genome-wide explanation of the expression data. We evaluate the method on two Saccharomyces cerevisiae gene expression data sets, showing that our approach is better than a standard one at recovering known motifs and at generating biologically coherent modules. We also combine our results with binding localization data to obtain regulatory relationships with known transcription factors, and show that many of the inferred relationships have support in the literature.