基于生物信息学对脊髓损伤后关键微小RNA与转录因子的筛选及其靶基因预测

Identification of the key microRNAs,transcription factors and target genes for spinal cord injury based on bioinformatics analysis

目的探讨脊髓损伤(SCI)后关键的微小RNA(miRNAs)与转录因子(TFs)并进一步了解miRNAs、TFs与靶基因的互作关系。方法从基因表达综合数据库(GEO)下载基因表达谱(GSE19890), 将差异倍数(log2FC)≥1和错误发现率(FDR)≤0.05作为标准阈值, 通过对微阵列数据分析筛选出差异表达的miRNAs(DEmiRNAs)。预测DEmiRNAs靶基因后分别进行京都基因与基因组百科全书(KEGG)通路和基因本体论(GO)功能富集分析, 接着基于TFs-靶基因互作分析确定关键的TFs, 根据靶基因的蛋白-蛋白互作网络分析确定特殊的DEmiRNA。结果通过对数据的分析, 分别与对照组相比, SCI后1 d出现5个下调基因和74个上调基因, 3 d后有118个下调基因和21个上调基因, 7 d后有450个下调基因和11个上调基因。韦恩在线分析筛选出7个重叠的DEmiRNAs参与了SCI后的表达调控。KEGG富集分析主要涉及细胞衰老、胰岛素抵抗和促性腺激素释放激素(GnRH)等信号通路, GO富集分析主要涉及RNA聚合酶Ⅱ启动子的转录正调控、基因表达的正调控和大脑发育等。通过TFs-靶基因互作分析发现了6个TFs, 比较10个Hub靶基因后我们发现了特殊的DEmiRNA(miR-124-3p)。结论 7个DEmiRNAs与6个TFs在SCI后可能通过调控靶基因的表达起着关键作用, 其中miR-124-3p通过调控特殊的靶基因产生了重要影响。

Objective To identify key miRNAs(microRNAs)and transcription factors(TFs)as-sociated with spinal cord injury(SCI)and further study the interactive relationship of miRNAs,TFs and target genes.Methods The array data of CSE19890 were downloaded from the gene expression omnibus(GEO)database.The expression differences were characterized by log2FC(Ilog2fold changel≥1)and false discovery rate(FDR≤0.05).Subsequently,the differentially expressed miRNAs(DEmiRNAs)were screened and analyzed after SCI based on the array data.After target genes of the overlapping DEmiRNAs were predicted,kyoto encyclopedia of genes and genomes(KEGG)and gene ontology(GO)analysis were performed respectively.Then,the key TFs were predicted by TFs-target genes interaction analysis.Also,the protein-protein interaction(PPI)network analysis of target genes was performed to identify the specific DEmiRNA.Results From the array data after SCI,compared with the control group respectively,there were 5 down-regulated genes and 74 up-regulated genes at 1 day after SCI,118 down-regulated genes and 21 up-regulated genes at 3 days after SCI,and 450 down-regulated genes and 11 up-regulated genes at 7 days after SCI.And then the 7 overlapping DEmiRNAs were identified based on Venn.KEGG enrich-ment analysis revealed that the involved mainly pathways in cellular senescence,insulin resistance and GnRH(Gonadotropin Releasing Hormone)signaling pathway.GO enrichment analysis mainly revealed pos-itive regulation of transcription from RNA polymerase II promoter,positive regulation of gene expression and brain development.Meanwhile,6 TFs were found based on TF-target gene interaction network analysis.After the 10 Hub target genes were compared,we determined specific DEmiRNA(miR-124-3p).Conclusion The 7 key DEmiRNAs and 6 TFs may play an important role by regulating target genes expression after SCI.Meanwhile,miR-124-3p may produce a huge impact after SCI by regulating special target genes.