基于GEO数据库探索成釉细胞瘤与牙源性角化囊肿间差异基因

摘要/Abstract

摘要： 目的　探索成釉细胞瘤与牙源性角化囊肿间的差异基因，并进一步分析其功能，最终探寻成釉细胞瘤侵袭生长的机制。方法　从GEO数据集下载基因芯片数据GSE38494，运用R语言中的LIMMA数据包进行成釉细胞瘤和牙源性角化囊肿间的差异基因分析。借助DAVID数据库对差异基因进行GO分析和KEGG通路富集分析。STRING网站进行差异基因PPI网络构建，Cytoscape软件对其结果进行可视化，并使用MCODE插件筛选其中的关键基因。结果　通过分析，我们获得了335个差异基因。GO分析表明差异基因主要影响神经元分化、细胞粘附、生物粘附、与分化有关的细胞形态发生、细胞形态发生、细胞命运锁定等生物过程；富集的细胞组成主要是细胞外区、细胞外基质、细胞外组分、蛋白质类细胞外基质、细胞外基质结构的构成、突触等；富集的分子功能主要参与碳水化合物结合、肝素结合和转录因子活性等。KEGG通路分析发现差异基因主要参与细胞外基质-受体相互作用、轴突导向和癌症通路等信号通路。8个关键基因为SPARCL1、SERPINA1、ITIH2、IGFBP5、LAMB1、C3、GOLM1、FAM20A。结论　利用生物信息学筛选出成釉细胞瘤和牙源性角化囊肿间的差异基因。8个关键基因有望成为两者之间鉴别诊断的新标志物，并为成釉细胞瘤的研究提供了新思路。

关键词: GEO数据库, 成釉细胞瘤, 牙源性角化囊肿, 差异基因, 生物信息学分析

Abstract: Objective　To find the differential expression genes (DEGs) between ameloblastoma and odontogenic keratocyst, analyze their function, and explore the mechanism of ameloblastoma invasion and growth. Methods The gene chip data set GSE38494 was downloaded from GEO database. The LIMMA packets was used to analyze the differential expression genes between ameloblastoma and odontogenic keratocyst. Then the Database for Annotation, Visualization and Integrated Discovery (DIVID) was employed to analyze Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The PPI network of differential expression genes was constructed on Search Tool for the Retrieval of Interacting Genes (STRING) website. The results were visualized by Cytoscape software, and the hub genes were screened by MCODE plug-in. Results 335 differential genes were identified. GO analysis showed that differential genes mainly affected neuronal differentiation, cell adhesion, biological adhesion, cell morphogenesis involved in differentiation, cell fate commitment and other biological processes. Cell component enrichment was mainly involved in extracellular domain, extracellular matrix, extracellular region, proteinaceous extracellular matrix, component and synapse of extracellular matrix structure and so on. The molecular function of enrichment was mainly involved in carbohydrate binding, heparin binding and transcription factor activity. KEGG pathway analysis showed that differential genes were mainly engaged in signaling pathways such as ECM-receptor interaction, axon orientation and pathway in cancer. The 8 hub genes were SPARCL1, SERPINA1, ITIH2, IGFBP5, LAMB1, C3, GOLM1 and FAM20A. Conclusion The DEGs between ameloblastoma and odontogenic keratocyst are screened out by means of bioinformatics. The 8 hub genes are expected to become new markers for differential diagnosis between ameloblastoma and odontogenic keratocyst, and provide new ideas for studies on ameloblastoma.

Key words: GEO database, ameloblastoma, odontogenic keratocyst, differential expression genes, bioinformatics analysis

中图分类号:

R739.82

兰天俊刘鑫陈之锋. 基于GEO数据库探索成釉细胞瘤与牙源性角化囊肿间差异基因[J]. 口腔医学, 2020, 40(11): 1009-1014.

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