肾透明细胞癌基因表达谱芯片的生物信息学分析

Bioinformatics analysis of clear cell renal cell carcinoma gene expression microarray

目的利用生物信息学的方法分析肾透明细胞癌(ccRCC)相关基因功能富集、通路及关键基因的临床意义。方法从TCGA和GEO下载ccRCC的RNA测序数据和芯片数据,利用R语言筛选出差异基因。然后利用metascape进行通路和功能富集,利用STRING网站和Cytoscape软件构建蛋白质-蛋白质相互作用(PPI)网络,同时从PPI网络中筛选出关键基因。最后利用OncoLnc网站对CCL5、TYROBP、LILRB2和MMP9做生存分析。结果总共筛选出660个差异基因,这些差异基因与白细胞迁移、细胞黏附调节和免疫应答正调节等通路密切相关。在PPI网络中,得到两个意义显著的功能模块和15个关键基因。在这15个关键基因中,CCL5、TYROBP、LILRB2和MMP9表达的高低与ccRCC患者的生存率明显相关。结论通过对ccRCC基因表达谱芯片的生物信息学分析发现,CCL5、TYROBP、LILRB2和MMP9基因可能在ccRCC的发生发展过程中起重要作用。

Objective The bioinformatics methods were used to analyze the pathways and gene in clear cell renal cell carcinoma （ccRCC） and to analyze the clinical significance of the hub genes.Methods RNA sequencing data and microarray data of ccRCC were downloaded from TCGA and GEO, and the differential genes were screened by R software. Metascape was used to enrich the pathway and function, using the STRING website and Cytoscape software to construct a protein-protein interaction （PPI） network, while screening out key genes from the web. Finally, CCL5, TYROBP, LILRB2 and MMP9 were analyzed by OncoLnc.Results A total of 660 differentially expressed genes were screened out. These differentially expressed genes were closely related to the pathways of leukocyte migration, cell adhesion regulation and immune response regulation. In the PPI network, two significant modules and 15 key genes were obtained. Among the 15 key genes, the expression level of CCL5, TYROBP, LILRB2 and MMP9 was significantly correlated with the survival rate of patients with ccRCC. Conclusions The 4 key genes of CCL5, TYROBP, LILRB2 and MMP9 may play a significant role in the development of ccRCC.