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Identifying gene expression profile of spinal cord injury in rat by bioinformatics strategy

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Abstract

Spinal cord injury (SCI) leads to the loss of sensory, motor, and autonomic function. We aimed to identify the therapeutic targets of-SCI by bioinformatics analysis. The gene expression profile of GSE20907 was downloaded from gene expression omnibus database. By comparing gene expression profiles with control samples, we screened out several differentially expressed genes (DEGs) in 3 days, 2 weeks and 1 month post-SCI. The pathway enrichment and protein–protein interaction (PPI) network analysis for the identified DEGs were performed. Then, transcription factors and microRNAs for DEGs were predicted. We found that up-regulated DEGs mainly participated in cell cycle, oxidative phosphorylation and immune-related pathways; while down-regulated DEGs were mainly involved in oxidative phosphorylation and central nervous system disease signaling pathways. In the constructed PPI network, Bub1, Vascular endothelial growth factor, Topoisomerase IIα (TOP2a) and Cdc20 showed better correspondence with cell cycle, repair system and nerve system. Furthermore, the up-regulated genes (Arpc1b, CD74 and Brd2) significantly mapped to the target genes of transcription factors. The down-regulated genes of 3 days post-injury and the up-regulated genes of 2 weeks post-injury were significantly enriched as the target genes of microRNAs (miR-129 and miR-124). In conclusion, our results may provide guidelines to discuss the collaboration of PPI network in carcinogenesis of SCI.

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Acknowledgments

The article was sponsored by Program of Shanghai Subject Chief Scientist (2012XD1404400) and International Science & Technology Cooperation Program of China (2011DFB30010).

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Authors and Affiliations

  1. Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China

    Lingjing Jin

  2. Department of Spine Surgery, Shanghai Tongji Hospital, Tongji University School of Medicine, Xin-Cun Road 389, Shanghai, 200065, China

    Zhourui Wu, Wei Xu, Xiao Hu & Liming Cheng

  3. Department of Regenerative Medicine, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China

    Jin Zhang

  4. Translational Stem Cell Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China

    Zhigang Xue

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  1. Lingjing Jin
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  2. Zhourui Wu
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  4. Xiao Hu
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  5. Jin Zhang
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  6. Zhigang Xue
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  7. Liming Cheng
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Correspondence to Zhigang Xue or Liming Cheng.

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Lingjing Jin and Zhourui Wu should be the co-first author.

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Jin, L., Wu, Z., Xu, W. et al. Identifying gene expression profile of spinal cord injury in rat by bioinformatics strategy. Mol Biol Rep 41, 3169–3177 (2014). https://doi.org/10.1007/s11033-014-3176-8

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  • DOI: https://doi.org/10.1007/s11033-014-3176-8

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