用生物信息学方法分析鉴定肺腺癌中的hub基因

Analysis and Identification of Hub Gene in Lung Adenocarcinoma by Bioinformatics

从高通量基因表达数据库(Gene Expression Omnibus,GEO)中获得基因表达谱序列号,并使用R中的“limma”包对差异表达基因(Differentially Expressed Genes,DEGs)进行鉴定。为确定差异基因所涉及的生物学过程及信号通路,进行了基因本体论(Gene Ontology,GO)富集分析和基因组的京都百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析,研究发现DEGs主要与细胞外基质组织、细胞外结构组织和有丝分裂的细胞核分裂有关,其主要富集在补体和凝血级联、细胞外基质受体相互作用和黏着作用的通路上。采用蛋白质-蛋白质互作(Protein-Protein Interaction,PPI)网络分析得到了由716个DEGs网络节点和3759条边构成的PPI网络,并在其中初步筛选出20个hub基因。通过加权基因共表达网络分析(Weighted Gene Co-expression Network Analysis,WGCNA)从DEGs中得到了18个模块,对hub基因进行鉴定,筛选出17个hub基因。使用Oncomine数据库对hub基因在肺腺癌患者与正常人的表达情况进行Meta分析,共鉴定出16个hub基因与肺腺癌相关。对肺腺癌患者进行总体生存分析,发现hub基因高表达患者总生存期比低表达患者短。

Gene expression profiles were obtained from the Gene Expression Omnibus(GEO)database and the differentially expressed genes(DEGs)were identified using the‘limma’package in R.In order to determine the biological processes and signal pathways involved in differential genes,we conducted Gene Ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis.It was found that DEGs were mainly related to extracellular matrix tissue,extracellular structural tissue and mitotic nuclear division,and were mainly contained in the pathway of complement and coagulation cascade,ECM receptor interaction and adhesion.Subsequently,the protein-protein interaction network(PPI)analysis was used to obtain a PPI network consisting of 716 DEGs network nodes and 3759 edges,among which 20 hub genes were preliminarily screened.Through weighted gene co-expression network analysis(WGCNA),18 modules were obtained from DEGs,hub genes were identified,and 17 hub genes were screened.The Oncomine database was used to conduct meta-analysis on the expression of hub genes in patients with lung adenocarcinoma and normal people,and 16 hub genes were identified to be associated with lung adenocarcinoma.Upon analyzing the overall survival of patients with lung adenocarcinoma,we found that the overall survival of higher expression patients of all hub genes was significantly shorter than patients,with lower expression patients of all hub genes.