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肝细胞肝癌是死亡率较高的癌种之一。本研究旨在为HCC的发生发展机制研究提供更多数据支持,从而对HCC的基因治疗提供一定的理论基础。从GEO数据库检索下载肝癌患者芯片数据GSE62232,包括10个正常肝脏样本,81个HCC患者的肿瘤样本。用Limma包分析HCC肿瘤组织中与正常肝组织中差异表达基因。随后进行基因本体论(GO)和信号通路(KEGG)富集分析。Cytoscape的MCODE插件用于分析差异基因的蛋白质相互作用关系。并筛选出Hub基因并应用Kaplan-Meier分析其在肝癌患者中的总体存活率情况。筛选得到237个DEGs (82个上调基因和155个下调基因),主要富集在视黄醇代谢通路,P53信号通路和PPAR信号通路。从PPI网络中鉴定出2个关键子网络和29个Hub基因;并得到与肝癌患者预后不良相关的8个基因的生存曲线。本研究可为HCC的发生发展的机制研究和药物靶点提供新的研究方向。
Abstract：Hepatocellular carcinoma(HCC) is one of the cancers species with high mortality rates. The purpose of this study is to provide more data for the underlying mechanism of HCC, which could be useful for the research of gene therapy. The array data of GSE62232 was downloaded from GEO database, including 10 normal liver samples, and 81 HCC liver tumors corresponding to 81 patients. The differentially expressed genes(DEGs) in the HCC tumor tissues compared with the normal liver tissue were analyzed with limma package. The gene ontology(GO) and Kyoto Encyclopedia of Gene and Genomes pathway(KEGG) enrichment analyses were performed subsequently.The Molecular Complex Detection(MCODE) plug-in in Cytoscape was applied to identify protein-protein interaction(PPI) network of the DEGs. Hub genes were picked out and the Kaplan-Meier analysis for overall survival was also applied. 237 DEGs were identified(82 up-regulated and 155 down-regulated genes), which were enriched in retinol metabolism, P53 signaling pathway and PPAR signaling pathway. The top 2 modules and top 29 hub genes were identified from the PPI network; survival curves of 8 genes associated with poor prognosis in patients with liver cancer. This study could provide more data for the underlying mechanism and drug-target for HCC.
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基本信息:
DOI：10.13417/j.gab.039.004345
中图分类号:R735.7;Q811.4
引用信息:
[1]殷松娜,张翔,杜娟,等.生物信息学分析鉴定肝细胞癌中的关键基因和信号通路[J].基因组学与应用生物学,2020,39(09):4345-4352.DOI:10.13417/j.gab.039.004345.
基金信息:
陕西省教育厅专项项目(18JK0863);陕西省教育厅专项项目(18JK0869);; 延安大学博士科研启动项目(20504-0136);延安大学校级引导项目(205100114)共同资助
2020-09-25
2020-09-25