Bioinformatics analysis identifies hub genes and pathways in nasopharyngeal carcinoma
Bioinformatics analysis identifies hub genes and pathways in nasopharyngeal carcinoma
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生物信息学分析确定鼻咽癌的中心基因和通路
DOI：
10.3892/ol.2019.10707
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发表时间：
2019-10-01
期刊：
影响因子：
2.9
通讯作者：
Wang, Rensheng
中科院分区：
文献类型：
--
作者：
Liu, Kang;Kang, Min;Wang, Rensheng
本研究的目的是利用基因芯片技术筛选鼻咽癌相关基因并探讨其发生机制。GSE 12452和GSE 34573基因表达谱获自Gene Expression Omnibus（GEO）数据库。利用GEO 2 R获得差异表达基因（DEG）。此外，注释、可视化和集成发现数据库用于使用基因本体（GO）注释沿着京都基因和基因组百科全书（KEGG）对DEG进行途径富集分析。利用Cytoscape软件对蛋白质-蛋白质相互作用（PPI）网络进行了模块分析，并对枢纽基因的作用途径进行了研究。两个数据集中共有298个基因被确定为DEG。为了在功能上对这些DEG进行分类，我们获得了82个补充的GO术语沿着7个KEGG通路。随后，构建了由10个具有高度相互作用的枢纽基因组成的PPI网络。这些枢纽基因包括细胞周期蛋白依赖性激酶（CDK）1、染色体结构维持（SMC）4、着丝粒相关基因（KNTC）1、驱动蛋白家族成员（KIF）23、极光激酶A（AURKA）、ATAD（含有ATP酶家族AAA结构域）2，NDC 80动粒复合物组分，zeste 2多梳抑制复合物2亚基的增强子，BUB 1有丝分裂检查点丝氨酸/苏氨酸激酶和胞质分裂蛋白调节因子1。CDK 1、SMC 4、KNTC 1、KIF 23、AURKA和ATAD 2基因在受试者工作曲线中的曲线下面积较大，提示这些基因可能是鼻咽癌的诊断标志物。提示CDK 1、SMC 4、KNTC 1、KIF 23、AURKA和ATAD 2可能参与了鼻咽癌的发生发展。此外，它们还可作为鼻咽癌早期诊断的分子生物学标志物。
The aim of the present study was to identify genes associated with and the underlying mechanisms in nasopharyngeal carcinoma (NPC) using microarray data. GSE12452 and GSE34573 gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. GEO2R was utilized to obtain differentially expressed genes (DEGs). In addition, the Database for Annotation, Visualization and Integrated Discovery was used to perform pathway enrichment analyses for DEGs using the Gene Ontology (GO) annotation along with the Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, Cytoscape was used to perform module analysis of the protein-protein interaction (PPI) network and pathways of the hub genes were studied. A total of 298 genes were ascertained as DEGs in the two datasets. To functionally categorize these DEGs, we obtained 82 supplemented GO terms along with 7 KEGG pathways. Subsequently, a PPI network consisting of 10 hub genes with high degrees of interaction was constructed. These hub genes included cyclin-dependent kinase (CDK) 1, structural maintenance of chromosomes (SMC) 4, kinetochore-associated (KNTC) 1, kinesin family member (KIF) 23, aurora kinase A (AURKA), ATAD (ATPase family AAA domain containing) 2, NDC80 kinetochore complex component, enhancer of zeste 2 polycomb repressive complex 2 subunit, BUB1 mitotic checkpoint serine/threonine kinase and protein regulator of cytokinesis 1. CDK1, SMC4, KNTC1, KIF23, AURKA and ATAD2 presented with high areas under the curve in receiver operator curves, suggesting that these genes may be diagnostic markers for nasopharyngeal carcinoma. In conclusion, it was proposed that CDK1, SMC4, KNTC1, KIF23, AURKA and ATAD2 may be involved in the tumorigenesis of NPC. Furthermore, they may be utilized as molecular biomarkers in early diagnosis of NPC.