Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data.
Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data.
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DOI：
10.11234/gi1990.15.2_287
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发表时间：
2004
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影响因子：
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通讯作者：
Tho Hoan Pham;K. Satou;T. Ho
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文献类型：
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作者：
Tho Hoan Pham;K. Satou;T. Ho
未标记 在真核生物中，基因表达受到与启动子区域结合的各种转录因子的控制。转录因子可能发挥积极作用、消极作用或根本不发挥作用。它们的不同组合也可能激活或抑制基因表达，并形成转录调控网络。发现这样的调控网络是基因组生物学的一个核心挑战。在本研究中，我们首先在调控网络中定义了一种新的基序，即转录调控模块（TRM），其形式为因子集-->基因集，强调因子集组对基因组基因组的组合基因控制。其次，我们开发了一种基于封闭项集挖掘技术的有效方法，用于从因子 DNA 结合位点和基因表达谱数据中查找信息最丰富的两种 TRM：封闭 inf-TRM 和封闭 super-TRM。所有封闭的inf-TRM和封闭的sup-TRM的集合通常比所有TRM的集合小几个数量级，但不会丢失任何信息。当应用于酵母数据时，我们的方法产生的结果比以前的研究更紧凑、简洁和全面，以识别和解释调节器组合对基因组的转录作用。可用性补充文件：http://www.jaist.ac.jp/~h-pham/regulation/。
UNLABELLED In eukaryotes, gene expression is controlled by various transcription factors that bind to the promoter regions. Transcription factors may act positively, negatively or not at all. Different combinations of them may also activate or repress gene expression, and form regulatory networks of transcription. Uncovering such regulatory networks is a central challenge in genomic biology. In this study, we first defined a new kind of motifs in regulatory networks, transcriptional regulatory modules (TRMs), with the form factorset --> geneset, which emphasizes the combinatorial gene control of the group of factors factorset on the group of genes geneset. Second, we developed an efficient method based on a closed itemset mining technique for finding the two most informative kinds of TRMs, closed inf-TRMs and closed sup-TRMs, from factor DNA-binding sites and gene expression profiles data. The set of all closed inf-TRMs and closed sup-TRMs is often orders of magnitude smaller than the set of all TRMs but does not loss any information. When being applied to yeast data, our method produced results that are more compact, concise and comprehensive than those from previous studies to identify and interpret the transcriptional role of regulator combinations on sets of genes. AVAILABILITY Supplementary files: http://www.jaist.ac.jp/~h-pham/regulation/.