Screening of differentially expressed genes of middle cerebral artery occlusion with DNA microarray

Y.-D. Zhang, X.-H. Gu, R.-Y. Dai, Z. Chen, J. Zhou, X.-Z. He, H. Wu, H.-J. Yang, Y.-H. Zhang

Department of Neurosurgery, Institute of Surgery Research, DaPing Hospital, Third Military Medical University, Chongqing, China. zhanggxh68@sina.com

 

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• Neurology

OBJECTIVES: To screen differentially expressed genes of different days after cerebral artery occlusion and drug treatment, and identify related small drug molecules.

MATERIALS AND METHODS: The gene expression profile GSE35338 of cerebral artery occlusion was downloaded from Gene Expression Omnibus database, including a total of 14 samples. 5 samples are 1 day after cerebral artery occlusion (control), 3 samples are 7 days after cerebral artery occlusion and 3 samples are under lipopolysaccharide (LPS) treatment. Differentially expressed genes (DEGs) between different days after cerebral artery occlusion were screened (p < 0.05, FDR < 0.05, |logFC| > 1). The DEGs were then entered into the CMAP database and related small drug molecules were retrieved, followed by calculation of co-expression score of the genes and construction of co-expression-drug network. FuncAssociate software and DAVID were used to obtain the functional clusters of genes with p-value < 0.05 and FDR < 0.05.

RESULTS: Compared with the control group, 825, 1445, 218 DEGs and 4, 3, 2 most-related small drug molecules were respectively identified from 3, 7 days after cerebral artery occlusion and LPS treated group. Co-expression network was constructed and functional clusters were found to be 161, 146, and 6 in each group.

CONCLUSIONS: Our study provides some underlying biomarkers for cerebral artery occlusion under varied conditions and potential small drug molecules for treatment of cerebral artery occlusion.