MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes.
MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes.
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DOI：
10.2741/e659
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
Zhaohui S. Qin;M. Bilenky;Gang Su;Steven J. M. Jones
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文献类型：
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作者：
Zhaohui S. Qin;M. Bilenky;Gang Su;Steven J. M. Jones
收集所有转录因子 (TF) 及其调节基因（调节子）的综合目录对于理解基因调节非常重要。 TF 的序列特异性保守结合谱可以通过系统发育方法从全基因组序列中表征，并且已经发布了大量此类谱。对这些数据源的有效挖掘可以通过计算揭示新的功能元素。由于结合位点的可变性，有必要通过聚类来概括与同一 TF 相关的概况。总结的家族谱可有效识别未知的结合位点，从而进行基因共调控预测。在这里，我们报告 MotifOrganizer，这是一种基于可扩展模型的聚类算法，设计用于对从哺乳动物物种的大规模比较基因组学研究中识别出的基序进行分组。新算法允许对具有可变宽度的图案进行分组，并且新颖的两阶段操作方案进一步提高了可扩展性。与基于距离和基于单阶段模型的聚类工具相比，MotifOrgainzer 在模拟数据上表现出了良好的性能。对 cisRED 人类数据库中大约 150k 个基序的测试表明，MotifOrganizer 可以有效地对哺乳动物基序的整个基因组集进行聚类。
Assembling a comprehensive catalog of all transcription factors (TFs) and the genes that they regulate (regulon) is important for understanding gene regulation. The sequence-specific conserved binding profiles of TFs can be characterized from whole genome sequences with phylogenetic approaches, and a large number of such profiles have been released. Effective mining of these data sources could reveal novel functional elements computationally. Due to the variability of the binding sites, it is necessary to generalize profiles pertinent to the same TF by clustering. The summarized familial profile is effective in identifying unknown binding sites, thus lead to gene co-regulation prediction. Here we report MotifOrganizer, a scalable model-based clustering algorithm designed for grouping motifs identified from large scale comparative genomics studies on mammalian species. The new algorithm allows grouping of motifs with variable widths and a novel two-stage operation scheme further increases the scalability. MotifOrgainzer demonstrated favorable performance comparing to distance-based and single-stage model-based clustering tools on simulated data. Tests on approximately 150k motifs from the cisRED human database demonstrated that MotifOrganizer can effectively cluster whole genome sets of mammalian motifs.