Terai Goro, Takagi Toshihisa
INTEC Web and Genome Informatics Corp., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-8637, Japan.
Bioinformatics. 2004 May 1;20(7):1119-28. doi: 10.1093/bioinformatics/bth049. Epub 2004 Feb 5.
In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements.
We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter regions of at least the specified number of genes. Then, we find significant patterns based on the expression similarity of genes with promoter regions containing each of the extracted patterns. When we applied our method to Saccharomyces cerevisiae, we detected significant patterns overlooked by previous methods, thus demonstrating the utility of our method for analyses of eukaryotic gene regulation. We also suggest that several types of element organization exist: (i) those in which only the order of elements is important, (ii) order and distance both are important and (iii) only the combination of elements is important.
The program for extracting element patterns is available upon request.
在真核生物中，关于顺式调控元件组织的规则很复杂。它们有时会控制多种元件以及元件的位置限制。
我们提出了一种检测规则的方法，通过该方法元件的顺序受到限制。顺序限制表示为元件模式。我们提取至少在指定数量基因的启动子区域中出现的所有元件模式。然后，我们基于具有包含每个提取模式的启动子区域的基因的表达相似性来找到显著模式。当我们将我们的方法应用于酿酒酵母时，我们检测到了先前方法忽略的显著模式，从而证明了我们的方法在真核基因调控分析中的实用性。我们还表明存在几种类型的元件组织：（i）仅元件顺序重要的那些，（ii）顺序和距离都重要的那些，以及（iii）仅元件组合重要的那些。
提取元件模式的程序可根据要求提供。
