Analysis of differentially expressed genes in ductal carcinoma with DNA microarray

B.-H. Zhang, J. Liu, Q.-X. Zhou, D. Zuo, Y. Wang

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, P.R. China. bhzhang@bio.ecnu.edu.cn

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• Oncology

AIM: The aim of this study is to investigate the dysregulated biological functions that play important role in the occurrence and development of breast invasive ductal carcinoma (IDC).

MATERIALS AND METHODS: We downloaded the gene expression profile data from gene expression omnibus (GEO) database, including 42 disease samples and 143 adjacent histological normal samples. Significance analysis of microarrays (SAM) was employed to identify differentially expressed genes (DEGs) between the normal and disease samples. Gene ontology (GO) function enrichment analysis was based on Software DAVID, followed by KEGG pathway enrichment analysis. TRANSFAC database and HPRD database were employed to construct the transcriptional regulatory network (Tnet) and protein-protein interaction (PPI) network, respectively.

RESULTS: We got a total of 1769 genes significantly differentially expressed, including 907 up-regulated genes and 862 down-regulated genes. Functional analysis revealed that hormone-responsive genes are related with the occurrence of cancer. Then, we successfully constructed IDC-specific Tnet and PPI network with DEGs response to hormone and obtained some hub genes, such as FOS and PIK3R1, in these networks. Besides, ten modules were found in these networks.

CONCLUSIONS: Hormone-responsive genes and modules may play an important role in the occurrence and development of IDC. Based on the findings above, we got a preliminary understand of the occurrence, development and metastasis of the IDC and possibly provided effective information on the biogenesis of IDC.

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