Paper:
Language: English:

Extraction of Developmentally Important Genes from Microarray Data

A Reum Han^, Dong-Soo Kahng^, Tae Woo Ryu^*, Hyun S. Moon^**, Kwang Hyung Lee^, and Doheon Lee^

^*Department of BioSystems, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon, Korea
^**Department of ComputerScience, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon, Korea

Received: October 31, 2004

Accepted: December 25, 2004

Keywords: development, fruitfly, scale-free network, hub, local dense region

Journal ref: Journal of Advanced Computational Intelligence and Intelligent Informatics, Vol.9, No.3 pp. 277-281, 2005

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.

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