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Molecular Biology Reports

, Volume 41, Issue 5, pp 3169–3177 | Cite as

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

  • Lingjing Jin
  • Zhourui Wu
  • Wei Xu
  • Xiao Hu
  • Jin Zhang
  • Zhigang Xue
  • Liming Cheng
Article

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.

Keywords

Spinal cord injury Differentially expressed genes Protein–protein interaction network Transcription factors microRNA 

Notes

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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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Neurology, Shanghai Tongji HospitalTongji University School of MedicineShanghaiChina
  2. 2.Department of Spine Surgery, Shanghai Tongji HospitalTongji University School of MedicineShanghaiChina
  3. 3.Department of Regenerative MedicineTongji University School of MedicineShanghaiChina
  4. 4.Translational Stem Cell Center, Tongji HospitalTongji University School of MedicineShanghaiChina

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