Predicting rules on organization of cis-regulatory elements, taking the order of elements into account
Predicting rules on organization of cis-regulatory elements, taking the order of elements into account
复制标题
DOI：
10.1093/bioinformatics/bth049
复制
发表时间：
2004-05-01
期刊：
影响因子：
5.8
通讯作者：
Takagi, T
中科院分区：
文献类型：
--
作者：
Terai, G;Takagi, T
动机：在真核生物中，关于顺式调控元件的组织规则是复杂的。结果：我们提出了一种规则检测方法，该方法限制了元素的顺序。顺序限制被表示为元素模式。我们提取至少在指定数量的基因的启动子区域中出现的所有元素模式。然后，我们根据基因表达的相似性找到有意义的模式，启动子区域包含每个提取的模式。当我们将我们的方法应用于酿酒酵母时，我们发现了以前方法忽略的显著模式，从而证明了我们的方法在分析真核基因调控方面的有效性。我们还认为存在几种类型的元素组织：(I)只有元素的顺序是重要的，(Ii)顺序和距离都是重要的，(Iii)只有元素的组合是重要的。
Motivation: In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements.Results: 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.