Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity
Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity
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DOI：
10.1007/s003350010219
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发表时间：
2001-01-01
期刊：
影响因子：
2.5
通讯作者：
Werner, T
中科院分区：
文献类型：
--
作者：
Gailus-Durner, V;Scherf, M;Werner, T
基因表达是目前基因组分析的主要研究方向，有关基因表达调控机制和功能转录因子结合位点的实验数据也在不断增加。然而，对序列转录调控的注释跟不上序列数据库的指数级增长。利用单个启动子或增强子的详细实验数据来预测具有相似调控的基因，将为连接转录调控文献和序列数据库提供一种强有力的方法。为此，我们利用单个功能转录因子结合位点的信息构建了肌肉特异性基因的启动子和增强子模型，并用这些模型分析了EMBL的啮齿动物部分。对所有匹配的详尽评估显示每2到3个匹配都是肌肉相关基因。此外，即使在没有序列相似性的情况下，我们的基于模型的方法也可以检测到功能相关的调控区域。我们认为这种新方法是BLAST或FASTA数据库分析的实质性扩展，这些方法仅限于序列相似性。
Gene expression is presently a major focus in genome analysis, and the experimental data on regulatory mechanisms and functional transcription factor binding sites are steadily growing. However, the annotation of transcriptional regulation of sequences cannot keep pace with the exponential growth of sequence databases. Employing detailed experimental data of a single promoter or enhancer to predict genes with similar regulation would provide a powerful method to link the literature about transcriptional regulation and sequence databases. To this end, we used information on individual functional transcription factor binding sites to compose in silico promoter and enhancer models of muscle-specific genes and to analyze the rodents section of EMBL with these models. Exhaustive evaluation of all hits revealed every second to third match to be a muscle-associated gene. Moreover, functionally related regulatory regions were detected by our model-based approach even in the absence of sequence similarity. We believe that this new approach is a substanial extension to database analysis by BLAST or FASTA, which are restricted to sequence similarity.