摘要
目的利用生物信息学方法筛选结肠癌进展相关的差异表达基因(DEGs)。方法从GEO数据库下载GSE127069、GSE145626数据集,运用GEO在线分析工具GEO2R提取这两个数据集的原始数据,利用韦恩图在线分析工具筛选DEGs。利用基因功能注释在线工具DAVID对DEGs进行GO功能注释和KEGG通路富集分析;将获得的DEGs数据导入STRING数据库构建PPI网络,并通过CytoHubba插件筛选枢纽基因;利用GEPIA数据库验证枢纽基因在结肠癌组织与癌旁组织中的表达差异。结果经GEO2R筛选,共从GSE127069、GSE145626数据集中获得DEGs 142个,其中表达上调基因35个、表达下调基因107个。GO功能注释发现,这些DEGs的生物学过程主要涉及细胞外基质降解、氧化还原过程、细胞黏附,分子功能主要涉及钙离子结合、碳酸盐脱水酶活性,细胞组分主要涉及胞外区域、膜的组成;KEGG通路富集分析显示,筛选获得的DEGs主要涉及PI3K-Akt通路和代谢途径通路。通过CytoHubba插件筛选PPI网络中相互作用排名前10位的DEGs作为枢纽基因,分别为IL-6、GCG、SLC26A3、TIMP1、SPP1、TMIGD1、MYC、MMP3、MMP1、SLC9A2。结肠癌组织GCG、TMIGD1表达低于癌旁组织,TIMP1、SPP1、MYC、MMP3、MMP1表达高于癌旁组织(P均<0.05);而结肠癌组织与癌旁组织IL-6、SLC26A3、SLC9A2表达比较差异均无统计学意义(P均>0.05)。结论本研究共筛选出10个与结肠癌进展相关的枢纽基因,分别为IL-6、GCG、SLC26A3、TIMP1、SPP1、TMIGD1、MYC、MMP3、MMP1、SLC9A2。
Objective To screen out the differentially expressed genes(DEGs)of colon cancer by using bioinformatics method.Methods GSE127069 and GSE145626 were downloaded from GEO database,DEGs were analyzed by GEO2R and filtered by Venn.DAVID database,an online gene function annotation tool,was used for GO enrichment analysis and KEGG pathway analysis.The DEGs data were imported into STRING database to construct protein-protein interaction(PPI)network,and the hub genes were screened through CytoHubba.GEPIA database was used to verify the hub gene expression in the colon cancer tissues and adjacent tissues.Results A total of 142 DEGs were obtained from GSE127069 and GSE145626 using GEO2R online analysis tool,of which,35 were up-regulated and 107 were down-regulated.GO enrichment analysis showed that the main functions of DEGs involved extracellular matrix disassembly,oxidation-reduction process,cell adhesion,molecular functions of calcium ion binding and carbonate anhydrase activity,and cell components of extracellular regions and composition of membranes.KEGG signal pathway analysis suggested that the main functions of DEGs involved PI3K-Akt signaling pathway and metabolic pathways.The top ten hub genes in PPI network were screened out by CytoHubba,including IL-6,GCG,SLC26A3,TIMP1,SPP1,TMIGD1,MYC,MMP3,MMP1,and SLC9A2.The expression levels of GCG and TMIGD1 were found to be much lower in the colon cancer tissues than in the adjacent tissues,while the levels of TIMP1,SPP1,MYC,MMP3,and MMP1 were higher(all P<0.05).There was no significant difference in the expression levels of IL-6,SLC26A3,or SLC9A2 between the colon cancer and adjacent tissues(all P>0.05).Conclusion In this study,ten hub genes may be involved in the occurrence and progression of colon cancer,including IL-6,GCG,SLC26A3,TIMP1,SPP1,TMIGD1,MYC,MMP3,MMP1,and SLC9A2.
作者
王成吕
聂玉洁
潘润桑
朱兰
陈双会
陈辉
张湘燕
聂瑛洁
WANG Chenglyu;NIE Yujie;PAN Runsang;ZHU Lan;CHEN Shuanghui;CHEN Hui;ZHANG Xiangyan;NIE Yingjie(Department of Biomedicine,Medical College,Guizhou University,Guiyang 550025,China;不详)
出处
《山东医药》
CAS
2022年第1期15-19,共5页
Shandong Medical Journal
基金
国家自然科学基金资助项目(82060308)
贵州省科技计划项目(黔科合平台人才[2018]5801)
贵州省免疫疗法研究人才基地(黔人领办发〔2018〕4号)。
