Co-expression pattern from DNA microarray experiments as a tool for operon prediction

The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in particular the distance between open reading frames, has been used to predict if adjacent Escherichia coli genes are in an operon. While appreciably successful, these predictions need to be validated and refined experimentally. As a growing number of gene expression array experiments on E.coli became available, we investigated to what extent they could be used to improve and validate these predictions. To this end, we examined a large collection of published microarry data. The correlation between expression ratios of adjacent genes was used in a Bayesian classification scheme to predict whether the genes are in an operon or not. We found that for the genes whose expression levels change significantly across the experiments in the data set, the currently available gene expression data allowed ...

• Type: Journal
• Year: 2002
• Where: NAR
• Authors: Chiara Sabatti, Lars Rohlin, Min-Kyu Oh, James C. Liao
• Keywords: Gene Expression, NAR 2002, Operon, Prediction