Predicting transcription factor binding sites using local over-representation and comparative genomics.
Predicting transcription factor binding sites using local over-representation and comparative genomics.
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DOI：
10.1186/1471-2105-7-396
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发表时间：
2006-08-31
影响因子：
3
通讯作者：
Touzet H
中科院分区：
文献类型：
--
作者：
Defrance M;Touzet H
识别顺式调控元件对于理解基因表达至关重要，这突出了计算检测共表达或共调控基因中过度表达的转录因子结合位点（TFBS）的重要性。然而，这是一个具有挑战性的问题，特别是考虑到高等真核生物。我们已经开发了一种方法，名为TFM-Explorer，搜索局部过度TFBS在一组共调节基因，这是由位置权重矩阵的数据库提供的配置文件建模。该方法的新奇在于它利用了序列中的空间保守性，并支持多个物种。底层算法的效率及其对噪声的鲁棒性允许在大的异构数据集中检测到弱的调节信号。TFM-Explorer提供了一种有效的方法来预测相关序列中TFBS的过度表达。在人类、小鼠和大鼠基因组的各种实例中获得了有希望的结果。该软件可在以下网址公开获取。
Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs) in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms. We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory signals to be detected in large heterogeneous data sets. TFM-Explorer provides an efficient way to predict TFBS overrepresentation in related sequences. Promising results were obtained in a variety of examples in human, mouse, and rat genomes. The software is publicly available at .
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负鼠：共表达基因中代表性过多的转录因子结合位点的鉴定。
影响因子：
14.9
作者：
Sui, SJH;Mortimer, JR;Arenillas, DJ;Brumm, J;Walsh, CJ;Kennedy, BP;Wasserman, WW
通讯作者：
Wasserman, WW
影响因子：
5.8
作者：
Thijs, G;Lescot, M;Moreau, Y
通讯作者：
Moreau, Y
影响因子：
5.8
作者：
Johansson, Oe.;Alkema, W.;Lagergren, J.
通讯作者：
Lagergren, J.
影响因子：
9.8
作者：
Eddy, SR
通讯作者：
Eddy, SR
影响因子：
46.9
作者：
Tompa, M;Li, N;Zhu, Z
通讯作者：
Zhu, Z