腺泡状横纹肌肉瘤相关基因生物信息学分析

Bioinformatics analysis of the genes related to alveolar rhabdomyosarcoma

目的采用生物信息学方法预测与腺泡状横纹肌肉瘤(ARMS)相关的差异表达基因和信号通路。方法从基因表达综合数据库GEO中下载得到14组ARMS与正常对照组织产生的系列数据集GSE2787表达谱数据集,依据生物信息学分析方法,采用R语言分析工具筛选差异表达基因。注释、可视化和集成发现的数据库DAVID在线分析工具、R包、已知和预测的蛋白质-蛋白质相互作用STRING数据库及Cytoscape软件对差异表达基因进行基因功能、信号通路及蛋白-蛋白相互作用网络分析。结果共筛选出867个差异表达基因,表达上调基因737个,下调基因130个。蛋白-蛋白相互作用网络由752个节点和5 158个交互组成,网络分析列出蛋白相互作用网络的前35个中心节点蛋白。关键差异表达基因主要涉及RNA拼接等生物学过程、核糖核蛋白复合体等细胞组件、RNA结合等分子功能及剪接体信号通路。结论剪切刺激因子3(CSTF3)、剪接体相关蛋白同源体(CWC25)、Asp-Glu-Ala-Asp解旋酶5(DDX5)等差异表达基因及剪接体信号通路可能与ARMS的发生、发展密切相关。

Objective To explore the potential differentially expressed genes(DEGs)and signaling pathways associated with Alveolar rhabdomyosarcoma(ARMS)by bioinformatics analysis.Methods Gene expression profile of GSE2 787,generated from 14 pair ARMS and normal samples were downloaded from Gene Expression Omnibus(GEO)database for bioinformatics analysis.According to bioinformatics analysis method,R language analysis tool was used to screen DEGs.Annotation,visualization and integration of discovered databases DAVID online analysis tools,R package,known and predicted protein-protein interaction(PPI)STRING database and Cytoscape software were used for gene function,signal pathway and protein-protein interaction network analysis of DEGs.Results A total of 867 DEGs were identified,including 737 up-regulated DEGs and 130 down-regulated DEGs The PPI network was consisted of 752 nodes and 5 158 interactions.The top 35 central node proteins of PPI network were screened by network analysis.The key DEGs mainly involved in biological processes such as RNA splicing,cellular components such as ribonuclide protein complex,molecular functions such as RNA binding,and spliceosomal signaling pathways.Conclusion The DEGs such as CSTF3,CWC25,DDX5 and spliceosome signaling pathway may be closely associated with the progress of ARMS.