Regulation of gene expression in rats with spinal cord injury based on microarray data.
The present study aimed to investigate the molecular mechanisms of spinal cord injury (SCI) in rats. First, the differentially expressed genes (DGEs) were screened based on GSE45006 microarray data downloaded from Gene Expression Omnibus using the significant analysis of microarray (SAM) method. Screening was performed for DEGs which were negatively or possibly correlated with time and subsequently subjected to gene ontology (GO) functional annotation. Furthermore, pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes was also performed. In addition, a protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Finally, GeneCodis was used to seek transcription factors and microRNAs that are involved in the regulation of DEGs. A total of 806 DEGs were upregulated and 549 DEGs were downregulated in the rats with SCI. Cholesterol metabolism-associated genes (e.g. HMGCS1, FDFT1 and IDI1) were negatively correlated with time, while injury genes (e.g. SERPING1, C1S and RAB27A) were positively correlated with time after SCI. PCNA, MCM2, JUN and SNAP25 were the hub proteins of the PPI network. The transcription factors LEF1 and SP1 were observed to be associated with the regulation of two DEGs that were involved in the cholesterol-associated metabolism as well as injury responses. A number of microRNAs (e.g. miR210, miR-487b and miR-16) were observed to target cholesterol metabolism-associated DGEs. The hub genes PCNA, MCM2, JUN and SNAP25 presumably have critical roles in rats with SCI, and the transcription factors LEF1 and SP1 may be important for the regulation of cholesterol metabolism and injury responses following SCI.
Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China.
Guoqiang
G
Chen
Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China.
Xiutong
X
Fang
Department of Orthopedics, Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, P.R. China.
Meng
M
Yu
D000818:Animals; D002784:Cholesterol / Q000378:metabolism; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D050356:Lipid Metabolism / Q000235:genetics; D051821:Lymphoid Enhancer-Binding Factor 1 / Q000235:genetics / Q000378:metabolism; D048670:MAP Kinase Kinase 4 / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D046228:Microarray Analysis; D064111:Minichromosome Maintenance Complex Component 2 / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D018809:Proliferating Cell Nuclear Antigen / Q000235:genetics / Q000378:metabolism; D060066:Protein Interaction Maps; D051381:Rats; D015398:Signal Transduction; D016329:Sp1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D013119:Spinal Cord Injuries / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D050825:Synaptosomal-Associated Protein 25 / Q000235:genetics / Q000378:metabolism
C497575:Lef1 protein, rat; D051821:Lymphoid Enhancer-Binding Factor 1; D035683:MicroRNAs; D018809:Proliferating Cell Nuclear Antigen; C494210:Snap25 protein, rat; D016329:Sp1 Transcription Factor; D050825:Synaptosomal-Associated Protein 25; D002784:Cholesterol; D048670:MAP Kinase Kinase 4; D064111:Minichromosome Maintenance Complex Component 2