Extraction of Developmentally Important Genes from Microarray Data

Abstract

Using microarray data on 4,028 genes during the lifecycle of Drosophila melanogaster, we constructed gene expression networks for 4 developmental stages of the fruitfly: egg and early embryo, embryo, larva, and pupa. The network for each stage showed a scale-free property with 0.85 < γ < 1.85 showing one or two giant clusters and many small clusters. Since hubs are thought to bring relatively dramatic changes in a network, we assumed hubs can be effective targets of medical treatments and/or drugs. Accordingly, we analyzed hub genes with a high degree for all networks. We found many previously studied genes that play crucial roles in each stage. We also assigned the biological process of gene ontology (GO) to genes in local dense regions of a cluster centered on hubs and found several enriched functions that are the keys to understand the effects of hubs.