基于GEO和TCGA数据筛选和鉴定食管鳞状细胞癌关键枢纽基因

Screening and Identifying the Hub Genes in Esophageal Squamous Cell Carcinoma Based on GEO and TCGA Data

[目的]基于GEO和TCGA数据库中的食管鳞状细胞癌的转录组数据,利用生物信息学方法筛选和鉴定食管鳞状细胞癌的关键枢纽基因。[方法]下载GEO中食管鳞状细胞癌数据集GSE17351和TCGA中的食管鳞状细胞癌RNA-seq数据,利用R软件Limma程序包筛选差异表达基因;利用ClusterProfiler程序包对差异基因进行GO分析和KEGG信号通路富集;利用STRING工具分析差异基因编码蛋白之间的相互作用网络并用Cytoscape软件进行可视化展示;利用Cytoscape的Cytohubba插件分析关键枢纽基因;利用K-M plotter分析关键枢纽基因的预后价值。[结果]通过GEO和TCGA筛选共得到167个共同差异表达基因;差异基因主要与核分裂、ATPase活性和DNA解旋酶活性等GO过程相关,且显著富集于DNA细胞周期、DNA复制、错配修复、卵母细胞减数分裂、ECM-受体相互作用、p53及Wnt等信号通路;一共筛选得到10个关键枢纽基因,其中BUB1、MAD2L1、NUF2、KIF18A、CENPK、CENPN、CENPQ和SPC25等8个基因与食管鳞状细胞癌患者的预后呈显著负相关。[结论]本研究经筛选得到了10个食管鳞状细胞癌关键枢纽基因,其中8个与预后相关,为食管鳞状细胞癌的分子机制研究和预后判断提供了潜在的靶点。

【Objective】To screen and identify the key pivotal genes of ESCC by bioinformatics methods based on transcriptome data of ESCC from geo and TCGA databases.【Methods】GSE17351 dataset and RNA-seq data of ESCC were downloaded from GEO and TCGA databases.Then Limma package of R software was applied to screen differentially expressed genes;ClusterProfiler package was used to perform GO analysis and KEGG Pathway enrichment;STRING tool was used to analyze the interaction network among proteins encoded by differential genes and the interactome was visualized by Cytoscape software;Cytoscapes Cytohubba plug-in was subjected to analyze key hub genes among interactome;The prognostic values of hub genes were analyzed by K-M plotter.[Results] A total of 167 differentially expressed genes were screened by GEO and TCGA;The differentially expressed genes were mainly related to GO processes such as mitosis,ATPase activity and DNA helicase activity,and were significantly enriched in DNA cell cycle,DNA replication,mismatch repair,oocyte meiosis,ECM receptor interaction,p53 and Wnt signaling pathways;A total of 10 key genes were screened,including BUB1,MAD2L1,NUF2,KIF18A,CENPK XENPN XENPQ and SPC25,which were negatively correlated with the prognosis of patients with ESCC.【Conclusion】Ten key pivotal genes of ESCC were screened,and eight of them were related to prognosis,which provided potential targets for molecular mechanism research and prognosis judgment of ESCC.