Yao Shenghui, Liu Taifeng
Department of Gynecology, The First People's Hospital of Xuzhou, Xuzhou, Jiangsu 221000, P.R. China.
Department of Medical Oncology, The First People's Hospital of Xuzhou, Xuzhou, Jiangsu 221000, P.R. China.
Oncol Lett. 2018 Jun;15(6):8319-8324. doi: 10.3892/ol.2018.8403. Epub 2018 Mar 30.
The aim of the present study was to identify the differentially expressed genes between cervical intraepithelial neoplasias (CIN) and adjacent normal tissue, and to construct a protein-protein interaction (PPI) network. A CIN dataset was obtained from Gene Expression Omnibus, and data of gene expression in CIN and adjacent normal tissue were extracted from GSE64217. The differentially expressed genes were selected using software package and heat map was drawn using the 'pheatmap' package. The selected differentially expressed genes were subjected to PPI, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using Cytoscape, Database for Annotation, Visualization and Integrated Discovery, STRING and KOBAS. In the present study, 287 genes were differentially expressed between CIN and adjacent normal tissue, of which 170 were significantly upregulated and 118 genes were significantly downregulated (P<0.00001, fold-change >6). A differential gene expression network map was constructed to show the interactions of 30 protein products encoded by differentially expressed genes using STRING software. In particular, the key gene, , was identified using Cytoscape software. The KEGG pathway analysis revealed that the differential genes were mainly involved in several pathways, including 'glutathione metabolism', 'arachidonic acid metabolism', and 'pentose phosphate pathway'. Results of the GO analysis showed that differential genes were enriched in different subsets. Specifically, small proline-rich protein 2E and 3, distal-less homeobox 5, epithelial membrane protein 1, cornifelin, periplakin, homeobox protein Hox-A13, estrogen receptor α, transglutaminase 1, small proline-rich protein 2A, Rh C glycoprotein, tumor protein p63, TGM3, homeobox B5 and small proline-rich protein 2D were enriched in 'epithelial cell differentiation', which affected the differentiation of epithelial cells. In conclusion, 287 differentially expressed genes were identified successfully. The key gene was identified based on the results of PPI, GO and KEGG analyses, and functional annotation and pathway analysis were also performed. Our study provides the basis for further studies on the interaction among differentially expressed genes.
本研究的目的是鉴定宫颈上皮内瘤变（CIN）与相邻正常组织之间的差异表达基因，并构建蛋白质-蛋白质相互作用（PPI）网络。从基因表达综合数据库（Gene Expression Omnibus）获取CIN数据集，并从GSE64217中提取CIN和相邻正常组织中的基因表达数据。使用软件包选择差异表达基因，并使用“pheatmap”包绘制热图。使用Cytoscape、注释、可视化和综合发现数据库（Database for Annotation, Visualization and Integrated Discovery）、STRING和KOBAS对选定的差异表达基因进行PPI、基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析。在本研究中，CIN与相邻正常组织之间有287个基因差异表达，其中170个显著上调，118个基因显著下调（P<0.00001，变化倍数>6）。使用STRING软件构建差异基因表达网络图谱，以显示由差异表达基因编码的30种蛋白质产物的相互作用。特别地，使用Cytoscape软件鉴定了关键基因。KEGG通路分析显示，差异基因主要参与几种通路，包括“谷胱甘肽代谢”、“花生四烯酸代谢”和“磷酸戊糖途径”。GO分析结果表明，差异基因在不同亚组中富集。具体而言，富含脯氨酸的小蛋白2E和3、远端缺失同源盒5、上皮膜蛋白1、角质化蛋白、周膜蛋白、同源盒蛋白Hox-A13、雌激素受体α、转谷氨酰胺酶1、富含脯氨酸的小蛋白2A、Rh C糖蛋白、肿瘤蛋白p63、TGM3、同源盒B5和富含脯氨酸的小蛋白2D在“上皮细胞分化”中富集，这影响上皮细胞的分化。总之，成功鉴定了287个差异表达基因。基于PPI、GO和KEGG分析结果鉴定了关键基因，并进行了功能注释和通路分析。我们的研究为进一步研究差异表达基因之间的相互作用提供了基础。
