Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and 
filamentous fungi to nematodes, plants, and mammals. In plants, several examples 
of operon-like gene clusters involved in metabolic pathways have recently been 
characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin 
biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis 
thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene 
clusters are defined by their co-regulation or neighboring positions within 
immediate vicinity of chromosomal regions. A comprehensive analysis of the 
expression of neighboring genes therefore accounts a crucial step to reveal the 
complete set of operon-like gene clusters within a genome. Genome-wide 
prediction of operon-like gene clusters should contribute to functional 
annotation efforts and provide novel insight into evolutionary aspects acquiring 
certain biological functions as well. We predicted co-expressed gene clusters by 
comparing the Pearson correlation coefficient of neighboring genes and randomly 
selected gene pairs, based on a statistical method that takes false discovery 
rate (FDR) into consideration for 1469 microarray gene expression datasets of A. 
thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters 
in total. We predicted 34 statistically significant gene clusters consisting of 
3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional 
relationships among genes in individual clusters were estimated by sequence 
similarity and functional annotation of genes. Duplicated gene pairs (determined 
based on BLAST with a cutoff of E<10(-5)) are included in 27 clusters. Five 
clusters are associated with metabolism, containing P450 genes restricted to the 
Brassica family and predicted to be involved in secondary metabolism. 
Operon-like clusters tend to include genes encoding bio-machinery associated 
with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, 
lipid and fatty-acid metabolism, and the lipid transfer system.