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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >CMStalker: A Combinatorial Tool for Composite Motif Discovery
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CMStalker: A Combinatorial Tool for Composite Motif Discovery

机译：CMStalker：用于发现复合图案的组合工具

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摘要

Controlling the differential expression of many thousands different genes at any given time is a fundamental task of metazoan organisms and this complex orchestration is controlled by the so-called encoding complex regulatory networks: several Transcription Factors bind to precise DNA regions, so to perform in a cooperative manner a specific regulation task for nearby genes. The prediction of these binding sites is still an open problem, notwithstanding continuous progress and activity in the last two decades. In this paper, we describe a new efficient combinatorial approach to the problem of detecting sets of cooperating binding sites in promoter sequences, given in input a database of Transcription Factor Binding Sites encoded as Position Weight Matrices. We present CMStalker, a software tool for composite motif discovery which embodies a new approach that combines a constraint satisfaction formulation with a parameter relaxation technique to explore efficiently the space of possible solutions. Extensive experiments with 12 data sets and 11 state-of-the-art tools are reported, showing an average value of the correlation coefficient of 0.54 (against a value 0.41 of the closest competitor). This improvements in output quality due to CMStalker is statistically significant.
机译：在任何给定时间控制成千上万个不同基因的差异表达是后生动物的基本任务，这种复杂的编排由所谓的编码复杂调节网络控制：几个转录因子与精确的DNA区域结合，因此可以在合作方式对附近基因进行特定的调控任务。尽管在过去的二十年中不断进步和活跃，但是对这些结合位点的预测仍然是一个悬而未决的问题。在本文中，我们描述了一种新的有效组合方法，可解决在启动子序列中检测协作结合位点集的问题，输入中给出了转录因子结合位点编码为位置权重矩阵的数据库。我们介绍了CMStalker，这是一种用于复合图案发现的软件工具，体现了一种新方法，该方法将约束满足公式与参数松弛技术相结合，以有效地探索可能的解决方案的空间。报告了使用12个数据集和11个最新工具的广泛实验，显示相关系数的平均值为0.54（最接近竞争对手的值为0.41）。由于CMStalker，输出质量的改善在统计上是显着的。

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