title: Identifying gene expression profile of spinal cord injury in rat by bioinformatics strategy.
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.
authors.affiliation: Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
authors.forename: Lingjing
authors.initials: L
authors.lastname: Jin
authors.forename: Zhourui
authors.initials: Z
authors.lastname: Wu
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.forename: Xiao
authors.initials: X
authors.lastname: Hu
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Xue
authors.forename: Liming
authors.initials: L
authors.lastname: Cheng
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D035683:MicroRNAs / Q000235:genetics; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D051381:Rats; D015398:Signal Transduction; D013119:Spinal Cord Injuries / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors