PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches

被引：15

作者：

Fujibuchi, W ^{[1
]}

Anderson, JSJ ^{[1
]}

Landsman, D ^{[1
]}

机构：

[1] NIH, Natl Lib Med, Natl Ctr Biotechnol Informat, Computat Biol Branch, Bethesda, MD 20894 USA

来源：

NUCLEIC ACIDS RESEARCH | 2001年 / 29卷 / 19期

关键词：

D O I：

10.1093/nar/29.19.3988

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naive consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data.

引用

页码：3988 / 3996

页数：9