基于生物信息学方法对结直肠癌组织差异表达关键基因的筛选

Screening of key differentially expressed genes in colorectal cancer tissues based on bioinformatics method

目的使用生物信息学的方法筛选结直肠癌(CRC)发生发展中的关键基因。方法从基因表达数据库(GEO)中筛选并下载CRC组织及癌旁组织的3个基因芯片(GSE71187、GSE31905、GSE35279),使用GEO在线分析工具GEO2R筛选出基因芯片中的差异表达基因(DEGs),并使用Venn在线网站筛选共表达DEGs。将筛选出来的共表达DEGs在DAVID网站进行基因本体(GO)功能和KEGG通路富集分析,绘制蛋白—蛋白相互作用网络图(PPI)并分析PPI中的核心DEGs。在基因表达谱数据动态分析网页工具(GEPIA)中绘制核心DEGs影响患者总生存期的生存曲线,筛选出预后相关基因,并在GEPIA和GEO中对预后相关基因在CRC组织和癌旁组织中的表达进行验证,得到CRC发生发展中的关键基因。结果从3个基因芯片中筛选出DEGs 5664个,其中上调DEGs 2703个、下调DEGs 2961个,通过Venn图筛选出共表达DEGs 390个。对共表达差异基因进行GO功能分析、KEGG通路富集分析、PPI绘制及核心网络分析后,再次筛选出核心DEGs 66个。对核心DEGs进行生存曲线分析及表达量验证后,筛选出核心DEGs 6个;其中上调DEGs 2个,包括分泌型磷蛋白1(SPP1)、血小板反应蛋白2(THBS2);下调DEGs 4个,包括氯化物通道附件1(CLCA1)、接触蛋白3(CNTN3)、胰高血糖素(GCG)、酶原颗粒蛋白16(ZG16)。结论使用生物信息学的方法筛选出SPP1、THBS2、CLCA1、CNTN3、GCG、ZG16可能是CRC发生发展过程中的关键基因。

Objective To screen the key genes in the development and progression of colorectal cancer(CRC)by bioinformatics methods.Methods Three gene chips(GSE71187,GSE31905,GSE35279)in the CRC and adjacent tis⁃sues were selected and downloaded from the Gene Expression Omnibus(GEO)database.We used GEO2R online tools to screen the differentially expressed genes(DEGs)and Venn diagrams to pick out the co-expressed DEGs.The David online website was used to perform the Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment.Then we drew the protein-protein interaction(PPI)and analyzed the core DEGs.We drew the survival curve of core DEGs affecting the overall survival(OS)of CRC patients,and screened out prognostic-related genes on the Gene Expression Profiling Interactive Analysis(GEPIA)online website.Then we verified the expression of prognostic-related genes in CRC tissues and adjacent tissues in the GEPIA and GEO databases,and obtained the key genes in the development and progression of CRC. Results We screened out 5 664 DEGs from the three eligible gene chips,including 2 703 up-regulated DEGs and 2 961 down-regulated DEGs,and meanwhile 390 co-expressed DEGs were screened out by Venn diagram. Sixty-six core DEGs were screened out after performing GO function analysis,KEGG path⁃ way enrichment analysis,and STRING website PPI mapping and core network analysis. After the survival curve analysis and expression verification of core DEGs,6 core DEGs were selected out,including 2 up-regulated DEGs,secreted phos⁃ phoprotein 1(SPP1)and thrombospondin 2(THBS2),and 4 down-regulated DEGs,chloride channel accessory 1(CL⁃ CA1),contactin 3(CNTN3),glucagon(GCG),and zymogen granule protein 16(ZG16). Conclusion SPP1,TH⁃ BS2,CLCA1,CNTN3,GCG,and ZG16 screened out by bioinformatics methods may be the key genes in the development and progression of CRC.