基于上游基序对参与甲硫氨酸和磷酸盐代谢的酵母基因进行鉴别。

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs.

作者信息

Gonze Didier, Pinloche Sylvie, Gascuel Olivier, van Helden Jacques

机构信息

Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, CP 263, Campus Plaine, Blvd du Triomphe, B-1050 Bruxelles, Belgium.

出版信息

Bioinformatics. 2005 Sep 1;21(17):3490-500. doi: 10.1093/bioinformatics/bti558. Epub 2005 Jul 5.

DOI:10.1093/bioinformatics/bti558

PMID:15998664

Abstract

MOTIVATION

In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus.

RESULTS

We scanned upstream regions of methionine, phosphate and control genes with position-specific weight matrices for Pho4p, Met4p/Met28p/Cbf1p and Met31p/Met32p, and applied discriminant analysis to classify genes according to matrix matching scores. This analysis showed that matrix scores provided a good discrimination between phosphate, methionine and control genes. The optimal parameters have then been used to predict phosphate and methionine regulation at a genome scale. The genome-scale analysis predicts 37 genes as methionine-regulated and 40 as phosphate-regulated. We compare the predictive results with high throughput data and discuss the difference.

AVAILABILITY

The programs for sequence retrieval and analysis, as well as the complete data and results, are available on the website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/).

CONTACT

jvanheld@scmbb.ulb.ac.be

SUPPLEMENTARY INFORMATION

The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/

摘要

动机

在酵母中，甲硫氨酸和磷酸盐代谢分别由Met4p/Met28p/Cbf1p和Pho4p复合物调节。这些因子的结合位点共享一个共同的核心序列CACGTG。尽管Met4p/Met28p/Cbf1p和Pho4p共有序列相似，但我们仍基于假定的调控元件评估我们区分磷酸盐响应基因和甲硫氨酸响应基因的能力。

结果

我们用针对Pho4p、Met4p/Met28p/Cbf1p和Met31p/Met32p的位置特异性权重矩阵扫描了甲硫氨酸、磷酸盐和对照基因的上游区域，并应用判别分析根据矩阵匹配分数对基因进行分类。该分析表明，矩阵分数能够很好地区分磷酸盐、甲硫氨酸和对照基因。然后，我们使用最优参数在基因组规模上预测磷酸盐和甲硫氨酸的调控情况。基因组规模分析预测出37个基因受甲硫氨酸调控，40个基因受磷酸盐调控。我们将预测结果与高通量数据进行比较并讨论了差异。