Research article

Positive correlation between gene coexpression and positional clustering in the zebrafish genome

Yen Kaow Ng¹ , Wei Wu² and Louxin Zhang¹

¹Department of Mathematics, National University of Singapore, 2 Science Drive 2, Singapore 117543, Singapore

²Institute of Molecular and Cell Biology, Singapore 138673, Singapore

author email corresponding author email

BMC Genomics 2009, 10:42doi:10.1186/1471-2164-10-42

Published:	22 January 2009

Abstract

Background

Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation.

Results

The analyses show that neighbouring genes are significantly coexpressed in the zebrafish genome, and the coexpression level is influenced by the intergenic distance and transcription orientation. This fact is further supported by examining the coexpression level of genes within positional clusters in the neighbourhood model. There is a positive correlation between gene coexpression and positional clustering in the zebrafish genome.

Conclusion

The study provides another piece of evidence for the hypothesis that coexpressed genes do cluster in the eukaryotic genomes.