Regulatory element detection using correlation with expression
Regulatory element detection using correlation with expression
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DOI：
10.1038/84792
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发表时间：
2001-02-01
期刊：
影响因子：
30.8
通讯作者：
Siggia, ED
中科院分区：
文献类型：
--
作者：
Bussemaker, HJ;Li, H;Siggia, ED
我们在这里提出了一种新的计算方法，用于发现顺式调控元件，从而避免了基于表达谱对基因进行聚类的需要。该方法基于上游基序对基因的对数表达水平有附加贡献的模型，需要单个全基因组的表达比率集和每个基因的上游序列，并输出具有统计学意义的基序。对公开获得的酿酒酵母表达数据的分析揭示了几个新的假定的调控元件，其中一些似乎控制着孢子形成过程中基因的早期瞬时诱导。已知的基序通常具有较高的统计显著性。
We present here a new computational method for discovering cis-regulatory elements that circumvents the need to cluster genes based on their expression profiles. Based on a model in which upstream motifs contribute additively to the log-expression level of a gene, this method requires a single genome-wide set of expression ratios and the upstream sequence for each gene, and outputs statistically significant motifs. Analysis of publicly available expression data for Saccharomyces cerevisiae reveals several new putative regulatory elements, some of which plausibly control the early, transient induction of genes during sporulation. Known motifs generally have high statistical significance.