Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
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DOI：
10.1101/gr.076117.108
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发表时间：
2008-07-01
期刊：
影响因子：
7
通讯作者：
Shamir, Ron
中科院分区：
文献类型：
--
作者：
Linhart, Chaim;Halperin, Yonit;Shamir, Ron
我们对基序发现的计算任务做出了三方面的贡献，基序发现是描绘基因组调控图谱的关键组成部分：(1)我们构建了一个全面的、大规模的、公开的转录因子和microRNA靶基因集的纲要，这些基因集来自几种后生动物的不同高通量实验。我们使用纲要作为motif发现工具的基准。(2)我们开发了Amadeus，这是一个高效，用户友好的软件平台，用于基因组尺度的新基序检测，适用于广泛的基序发现任务。Amadeus在准确性、运行时间、输出信息和易用性方面对现有工具进行了改进，是唯一在后生动物纲要上获得高成功率的程序。(3)我们证明，通过基于全基因组定位或染色体分布（不使用预定义的目标集）搜索基序，Amadeus揭示了多种已知现象，以及新的调控基序。
We present a threefold contribution to the computational task of motif discovery, a key component in the effort of delineating the regulatory map of a genome: ( 1) We constructed a comprehensive large-scale, publicly-available compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments in several metazoans. We used the compendium as a benchmark for motif discovery tools. ( 2) We developed Amadeus, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks. Amadeus improves upon extant tools in terms of accuracy, running time, output information, and ease of use and is the only program that attained a high success rate on the metazoan compendium. ( 3) We demonstrate that by searching for motifs based on their genome- wide localization or chromosomal distributions ( without using a predefined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.