基于生物信息学筛选三阴性乳腺癌关键基因和通路

Screening Key Genes and Pathways in Triple-negative Breast Cancer by Bioinformatics Analysis

目的采用生物信息学分析,筛选与三阴性乳腺癌(triple-negative breast cancer,TNBC)发生发展相关的关键基因和通路。方法选取GEO(Gene Expression Omnibus)数据库中TNBC基因芯片数据集GSE76124及正常乳腺组织数据集GSE112825,应用R软件筛选差异表达基因。使用DAVID数据库对上述差异表达基因进行GO(Gene Ontology)功能分析及KEGG(Kyoto Encyclopedia of Genes and Genome)通路分析。应用STRING在线数据库和Cytoscape软件构建蛋白质相互作用(protein-protein interaction,PPI)网络,并筛选TNBC的hub genes、枢纽模块和seed genes。结果分析芯片数据,筛选得到1091个差异表达基因,GO和KEGG分析结果显示,差异表达基因与芳香类物质生物合成、杂环生物合成等过程有关,并富集在cancer通路、PI3K/AKT通路上。通过构建PPI网络筛选得到了10个hub genes、2个枢纽模块和19个seed genes。结论本研究筛选得到10个hub genes和19个seed genes,这些基因在TNBC的发生发展中可能存在潜在的作用,为下一步研究提供生物信息学分析参考。

Objective To screen key genes and pathways associated with tumorigenesis and progression of triple-negative breast cancer(TNBC)by using bioinformatics analysis.Methods Two gene expression profilings containing TNBC(GSE76124)and normal mammary(GSE112825)tissue samples were obtained from Gene Expression Omnibus(GEO).R software was used to identify differentially expressed genes.Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were further performed by DAVID.STRING and Cytoscape were used to construct protein-protein interaction(PPI)network.Furthermore,hub genes,core modules and seed genes were screened out.Results A total of 1,091 differentially expressed genes were screened out.The results of GO function analysis and KEGG pathway maps showed that these genes were associated with aromatic compound biosynthetic process,heterocycle biosynthetic process,and mainly enriched on the pathways in cancer and PI3K-Akt signaling pathway.We identifi ed 10 hub genes,2 core modules and 19 seed genes in PPI network.Conclusion A total of 10 hub genes and 19 seed genes were screened,which may play potential roles in the tumorigenesis and progression of TNBC.This study provids a bioinformatic analysis reference for further research.