Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.
Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.
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调节性DNA序列的某些统计特性及其在预测果蝇基因组中的调节区域的使用：蓬松的尾巴测试。
DOI：
10.1186/1471-2105-6-109
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发表时间：
2005-04-27
影响因子：
3
通讯作者：
Gilks, WR
中科院分区：
文献类型：
--
作者：
Abnizova, I;te Boekhorst, R;Walter, K;Gilks, WR
本文解决了识别远离基因的DNA顺式调控模块的问题。这方面的实验过程缓慢且成本高昂，计算方法也很困难，因为它们缺乏位置信息。我们提出了一种新的统计方法，即“毛尾检验”，来识别调控DNA。我们利用了调控DNA的基本信息特性之一：丰富的过度表达转录因子结合位点(TFBS)基序，尽管我们本身并不寻找特定的TFBS基序。尽管TFBS基序在调控DNA中的过度表达已经被许多算法所利用，但将调控DNA与其他基因组DNA区分开来仍然是一个困难的问题。我们表明，在所使用的数据中，我们的方法能够通过利用调控和其他DNA中相似词的概率分布之间的统计差异来区分顺式调控模块。我们的方法的潜在应用包括新基因组序列的注释和基序的发现。
This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information. We present a novel statistical method, the "fluffy-tail test", to recognise regulatory DNA. We exploit one of the basic informational properties of regulatory DNA: abundance of over-represented transcription factor binding site (TFBS) motifs, although we do not look for specific TFBS motifs, per se . Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. The potential application of our method includes annotation of new genomic sequences and motif discovery.
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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
影响因子：
5.6
作者：
Audit, B;Vaillant, C;Thermes, C
通讯作者：
Thermes, C
影响因子：
5.8
作者：
Johansson, Oe.;Alkema, W.;Lagergren, J.
通讯作者：
Lagergren, J.
影响因子：
7
作者：
Lifanov, AP;Makeev, VJ;Papatsenko, DA
通讯作者：
Papatsenko, DA
影响因子：
7
作者：
Ohler, U
通讯作者：
Ohler, U