A statistical analysis of the TRANSFAC database
A statistical analysis of the TRANSFAC database
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DOI：
10.1016/j.biosystems.2005.03.003
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发表时间：
2005-08-01
期刊：
影响因子：
1.6
通讯作者：
Su, C
中科院分区：
文献类型：
--
作者：
Fogel, GB;Weekes, DG;Su, C
转录因子是控制基因表达的关键调控元件。TRANSFAC（R）数据库代表了实验衍生的转录因子结合位点（TFBS）的最大库。了解TFBS，这通常是保守的进化过程中，帮助我们确定与人类健康和疾病相关的基因组区域，以及可能预测患者结果的区域。在这里，我们对TRANSFAC（R）数据库中的所有TFBS进行了统计分析。我们的分析表明，目前在TRANSFAC（R）中对TFBS核心区域的定义应该重新审视，以便更准确地理解“核心”的概念。“我们提供了对TFBS共有序列和核心区域的更合适定义的见解。这些修订后的定义提供了一个更好的理解转录因子-DNA结合的性质，并协助开发从头TFBS发现算法，以及发现已知TFBS的新变体。(c)2005爱思唯尔爱尔兰有限公司保留所有权利。
Transcription factors are key regulatory elements that control gene expression. The TRANSFAC (R) database represents the largest repository for experimentally derived transcription factor binding sites (TFBS). Understanding TFBS, which are typically conserved during evolution, helps us identify genomic regions related to human health and disease, and regions that might be predictive of patient outcomes. Here we present a statistical analysis of all TFBS in the TRANSFAC (R) database. Our analysis suggests that current definition of TFBS core regions in TRANSFAC (R) should be re-examined so as to capture a more precise notion of "cores." We offer insight into more appropriate definitions of TFBS consensus sequences and core regions. These revised definitions provide a better understanding of the nature of transcription factor-DNA binding and assist with developing algorithms for de novo TFBS discovery as well as finding novel variants of known TFBS. (c) 2005 Elsevier Ireland Ltd. All rights reserved.