Positional clustering and co-expression analysis of neighboring genes in the zebrafish genome

Abstract

Microarray experiments provide deep insight into molecular evolution and how structure and function interrelate in a genome.Our study investigates whether neighboring and clustering genes in the zebrafish genome are co-expressed using the Affymetrix microarray data. Tandem duplicated genes are found to have a higher degree of co-expression than other neighboring genes in the analysis.A further analysis of the data set relates to the effect of intergenic distance. A significant correlation between distance and co-expression is found.We also study the positional clustering of genes in the zebrafish genome. A significant trend for large clusters is recognized. A positive correlation between the significance of positional clustering and the degree of neighboring gene co-expression is also found in the genome.Finally, we study the co-expression of genes with their gene ontology information, and find that the molecular function plays an important role in the gene co-expression.