Screening of key genes associated with contused rat spinal cord with DNA microarray

X.-j. Chen, X.-q. Mou, Y.-g. Zou, Z.-y. Peng, J.-x. Yang

Department of Orthopedics, Affiliated Hospital of Traditional Chinese Medicine, Luzhou Medical College, Luzhou, China. orthluzhou@163.com

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• Orthopedics

OBJECTIVES: To identify key genes and novel potential therapeutic targets for contused spin cord injury through analyzing microarray data.

MATERIALS AND METHODS: Gene expression data set GSE2599 was downloaded from Gene Expression Omnibus, including 3 rat spinal cord injury (SCI) samples and 3 healthy controls. Data pre-treatment and differential analyses were performed with packages of R. Cluster analysis was done with gene expression values to globally present the difference between the two states. Functional enrichment analysis was performed for all the DEGs with DAVID tools. The most up- and down-regulated genes were picked out and their interactors were predicted with String. Pathway enrichment analysis was done with GENECODIS for all the genes in the network.

RESULTS: A total of 227 DEGs were screened out, 132 up-regulated genes and 145 down-regulated genes. Response to wounding, response to organic substance and defense response was the top 3 significant functional terms. APOBEC1 was the most up-regulated gene while HPD was the most down-regulated one. Their interactors were obtained and network was constructed. Pathway enrichment analysis revealed that tyrosine metabolism and other metabolism-related pathways were significantly over-represented.

CONCLUSIONS: A range of DEGs were revealed in present study, which could deepen the understandings about the mechanisms of SCI and guide future researches on treatment development.

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