A survey of motif discovery methods in an integrated framework.
A survey of motif discovery methods in an integrated framework.
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DOI：
10.1186/1745-6150-1-11
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发表时间：
2006-04-06
期刊：
影响因子：
5.5
通讯作者：
Drabløs F
中科院分区：
文献类型：
--
作者：
Sandve GK;Drabløs F
人们对调节元件的计算发现越来越感兴趣，并且已经提出了多种基序发现方法。计算基序发现已在酵母等简单生物体中取得了一些成功。然而，当我们转向具有更复杂基因组的高等生物时，需要更灵敏的方法。最近的几种方法试图整合额外的信息源，包括微阵列实验（基因表达和 ChlP 芯片）。人们也越来越认识到调节元件是组合发挥作用的，并且必须对这种组合行为进行建模才能成功发现主题。然而，众多的方法和途径使得人们很难充分了解该领域的现状。本文基于一个整合了所有相关元素的结构化且明确定义的框架，对 DNA 基序发现方法进行了调查。根据该框架讨论现有方法。调查显示，虽然没有一种方法能够考虑所有相关要素，但已经尝试了大量分别处理各种要素的不同模型。通常，所做的选择没有明确说明，因此很难比较不同的实现。此外，已使用的测试通常不具有可比性。因此，需要一个严格的框架和改进的测试方法来评估不同的方法，以便得出哪些方法最有前途。审稿人：本文由 Eugene V. Koonin、Philipp Bucher（由 Mikhail Gelfand 提名）和 Frank Eisenhaber 审阅。
There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success in simple organisms like yeast. However, as we move to higher organisms with more complex genomes, more sensitive methods are needed. Several recent methods try to integrate additional sources of information, including microarray experiments (gene expression and ChlP-chip). There is also a growing awareness that regulatory elements work in combination, and that this combinatorial behavior must be modeled for successful motif discovery. However, the multitude of methods and approaches makes it difficult to get a good understanding of the current status of the field. This paper presents a survey of methods for motif discovery in DNA, based on a structured and well defined framework that integrates all relevant elements. Existing methods are discussed according to this framework. The survey shows that although no single method takes all relevant elements into consideration, a very large number of different models treating the various elements separately have been tried. Very often the choices that have been made are not explicitly stated, making it difficult to compare different implementations. Also, the tests that have been used are often not comparable. Therefore, a stringent framework and improved test methods are needed to evaluate the different approaches in order to conclude which ones are most promising. Reviewers: This article was reviewed by Eugene V. Koonin, Philipp Bucher (nominated by Mikhail Gelfand) and Frank Eisenhaber.
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DOI：
10.1073/pnas.231608898
发表时间：
2002-01-22
影响因子：
11.1
作者：
Berman, BP;Nibu, Y;Eisen, MB
通讯作者：
Eisen, MB
DOI：
10.1073/pnas.180265397
发表时间：
2000-08-29
影响因子：
11.1
作者：
Bussemaker, HJ;Li, H;Siggia, ED
通讯作者：
Siggia, ED
影响因子：
5.8
作者：
Donaldson, IJ;Chapman, M;Göttgens, B
通讯作者：
Göttgens, B
影响因子：
5.8
作者：
Aerts, S;Van Loo, P;De Moor, B
通讯作者：
De Moor, B
影响因子：
3
作者：
Corà D;Herrmann C;Dieterich C;Di Cunto F;Provero P;Caselle M
通讯作者：
Caselle M