基于数据库的胃癌相关差异表达基因筛选及生物学功能分析

Screening and biological function analysis of gastric cancer-related differentially expressed genes based on database

目的基于数据库筛选胃癌相关差异表达基因,分析胃癌相关差异表达基因的生物学功能及相关信号通路,探索胃癌相关核心差异表达基因与胃癌预后的关系。方法从GEO数据库选取胃癌相关基因芯片GSE79973、GSE54129,应用GEO2R分别筛选出两组芯片胃癌组织与正常胃黏膜组织的差异表达基因,取交集后得到共有差异表达基因。应用DAVID对差异表达基因进行生物学功能及信号通路分析。采用STRING构建差异表达基因蛋白互作网络,应用Cytoscape软件的MCODE插件筛选胃癌相关核心差异表达基因。对核心差异表达基因与胃癌预后的关系进行分析。结果相对于正常胃黏膜组织,胃癌组织差异表达基因共164个,其中42个上调、122个下调,主要存在于胞外区、蛋白细胞外基质、细胞外基质、细胞外外泌体等部位,主要涉及细胞外基质受体相互作用、局部黏附、蛋白质消化和吸收、细胞色素P450代谢等相关通路。初步筛选出13个胃癌相关核心基因(COL1A2、BGN、THBS2、FN1、THBS1、COL1A1、COL4A1、SPARC、COL11A1、COL6A3、COL12A1、TIMP1、SPP1),除THBS1外,其余12个与胃癌不良预后明显相关(P均<0.05)。结论与正常胃黏膜组织相比,胃癌组织相关差异表达基因共164个,其中42个上调、122个下调,主要在胞外区、蛋白细胞外基质等部位,主要与细胞外基质受体相互作用、局部黏附等相关通路有关;13个胃癌相关核心基因COL1A2、BGN、THBS2等中有12个与胃癌不良预后相关。

Objective To screen out the gastric cancer-related differentially expressed genes(DEGs),to analyze the biological function and signal pathways,and to explore the relationship between the expression of gastric cancer related core DEGs and the prognosis of gastric cancer.Methods Microarray data of gastric cancer GSE79973 and GSE54129 were downloaded from Gene Expression Omnibus database(GEO).We used GEO2 R to pick out DEGs between gastric cancer and normal gastric tissues.Then we obtained the common DEGs.We used DAVID to analyze the biological functions and signal pathways of DEGs.The protein-protein interaction(PPI)of these DEGs was constructed by STRING,then we imported it into Cytoscape.The core genes related to gastric cancer were screened out by MCODE plug-in.Finally,we analyzed the overall survival among those core genes.Results There were 164 DEGs in the two datasets,including 42 upregulated genes and 122 down-regulated genes.These DEGs mainly enriched in extracellular region,proteinaceous extracellular matrix,extracellular matrix,and extracellular exosome.They involved in ECM-receptor interaction,focal adhesion,protein digestion and absorption,cytochrome P450 metabolism and other related pathways.Preliminarily,we screened out13 core genes(COL1 A2,BGN,THBS2,FN1,THBS1,COL1 A1,COL4 A1,SPARC,COL11 A1,COL6 A3,COL12 A1,TIMP1,and SPP1)related to gastric cancer by MCODE,and 12 of 13 genes had a significantly worse prognosis.Except THBS1,the remaining 12 core genes were significantly associated with poor prognosis of gastric cancer(all P<0.05).Conclusions A total of 164 gastric cancer-related DEGs are screened out,including 42 up-regulated genes and 122 down-regulated genes.They are mainly located in extracellular region and proteinaceous extracellular matrix,which are related to ECM-receptor interaction,focal adhesion,and other related pathways,and 12 of 13 gastric cancer-related genes,such as COL1 A2,BGN,and THBS2 are associated with poor prognosis of gastric cancer.