摘要
目的 应用生物信息学方法分析和筛选与结肠癌(CC)诊断和预后相关的生物标志物.方法 从 GEO 数据库获取人类CC数据集GSE10950 和GSE29998.通过在线工具GEO2R和微生信在线数据平台绘制韦恩图并筛选数据集重叠的差异表达基因(DEGs).利用微生信在线数据分析平台对重叠 DEGs 进行基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析.通过String在线工具构建蛋白质-蛋白质互相作用(PPI)网络,并用Cytoscape软件 3.9.0 版及其插件分析PPI网络筛选出排名前 10 的关键基因.使用GEPIA数据库、HPA数据库和TIMER数据库进一步探索关键基因,并进行预后分析.结果 GSE10950 和GSE29998 两数据集中有1 215 个重叠DEGs,DEGs主要与DNA复制、细胞周期和嘌呤代谢等途径有关.经过PPI网络分析得到 10 个关键基因,使用GEPIA数据库进一步分析后,筛选出 4 个与CC预后相关的关键基因,分别是MYC、CTNNB1、HSP90AB1、NOP56.这 4 个基因都在CC中高表达,且均与CC患者不良预后有关.TIMER数据库显示其均与免疫浸润有关.结论 MYC、CTNNB1、HSP90AB1、NOP56可能是与CC发生发展有关的关键基因,可能是CC诊断标志物和潜在治疗靶点.
Abstract
Objective To apply bioinformatics methods to analyze and screen biomarkers related to the diagnosis and prognosis of colon cancer.Methods The human colon cancer datasets GSE10950 and GSE29998 were obtained from the gene expression omnibus(GEO)database,and the Wayne diagrams were plotted and screened for overlapping differentially expressed genes(DEGs)through the online tool GEO2R and the Microbiology online data platform.expressed genes(DEGs).The overlapping DEGs were enriched by Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)using Microbiotics online data analysis platform.Protein-protein interaction(PPI)networks were constructed by the STRING online tool,and the PPI networks were analyzed by Cytoscape software(version 3.9.0)and its plug-ins to screen the top ten key genes.The Gene Expression Profiling Interactive Analysis(GEPIA)database,Human Protein Atas(HPA)database and Tumor Immune Estimation Resource(TIMER)database were used.Resource(TIMER)database to further explore key genes and perform prognostic analysis.Results There were 1215 overlapping DEGs in both GSE10950 and GSE29998 datasets,and the DEGs were mainly associated with pathways such as DNA replication,cell cycle and purine metabolism.After PPI network analysis,10 key genes were obtained,and after further analysis using the GEPIA database,4 key genes associated with colon cancer prognosis were screened out,which were MYC,CTNNB1,HSP90AB1,and NOP56.all 4 genes were highly expressed in colon cancer,and all of them were associated with poor prognosis of patients with colon cancer.the TIMER database showed that they were all were associated with immune infiltration.Conclusion MYC,CTNNB1,HSP90AB1,and NOP56 may be key genes related to colon cancer development and may be diagnostic markers and potential therapeutic targets for colon cancer.
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