Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui, China (mainland).
Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, China (mainland).
Med Sci Monit. 2021 Jan 19;27:e927917. doi: 10.12659/MSM.927917.
BACKGROUND This bioinformatics study aimed to identify differentially expressed genes (DEGs) and protein-protein interaction (PPI) networks associated with functional pathways in ulcerative colitis based on 3 Gene Expression Omnibus (GEO) datasets. MATERIAL AND METHODS The GSE87466, GSE75214, and GSE48958 MINiML formatted family files were downloaded from the GEO database. DEGs were identified from the 3 datasets, and volcano maps and heat maps were drawn after R language standardization and analysis, respectively. Venn diagram software was used to identify common DEGs. PPI analysis of common DEGs was performed using the Search Tool for the Retrieval of Interacting Genes. Gene modules and hub genes were visualized in the PPI network using Cytoscape. Enrichment analysis was performed for all common DEGs, module genes, and hub genes. RESULTS A total of 90 DEGs were selected, which included 3 functional modules and 1 hub gene module. CXCL8 module genes were mainly enriched in cytokine-mediated signaling pathways and interleukin (IL)-10 signaling. CCL20 module genes were mainly enriched in the IL-17 signaling pathway and cellular response to IL-1. Hub gene modules mainly involved IL-10, IL-4, and IL-13 signaling pathways. CXCL8, CXCL1, and IL-1ß were the top 3 hub genes and were mainly involved in IL-10 signaling. CONCLUSIONS Bioinformatics analysis using 3 GEO datasets identified CXCL8, CXCL1, and IL-1ß, which are involved in IL-10 signaling, as the top 3 hub genes in ulcerative colitis. The findings from this study remain to be validated, but they may contribute to the further understanding of the pathogenesis of ulcerative colitis.
本生物信息学研究旨在基于 3 个基因表达综合数据集（GEO），鉴定与溃疡性结肠炎功能通路相关的差异表达基因（DEG）和蛋白质-蛋白质相互作用（PPI）网络。
从 GEO 数据库下载 GSE87466、GSE75214 和 GSE48958 MINiML 格式化家族文件。使用 R 语言标准化和分析后，分别绘制 DEG 的火山图和热图。使用 Venn 图软件识别共同的 DEG。使用 Search Tool for the Retrieval of Interacting Genes 对共同的 DEG 进行 PPI 分析。使用 Cytoscape 在 PPI 网络中可视化基因模块和枢纽基因。对所有共同的 DEG、模块基因和枢纽基因进行富集分析。
共选择了 90 个 DEG，包括 3 个功能模块和 1 个枢纽基因模块。CXCL8 模块基因主要富集在细胞因子介导的信号通路和白细胞介素（IL）-10 信号通路中。CCL20 模块基因主要富集在 IL-17 信号通路和细胞对 IL-1 的反应中。枢纽基因模块主要涉及 IL-10、IL-4 和 IL-13 信号通路。CXCL8、CXCL1 和 IL-1β是前 3 个枢纽基因，主要参与 IL-10 信号通路。
使用 3 个 GEO 数据集进行生物信息学分析，鉴定出参与 IL-10 信号通路的 CXCL8、CXCL1 和 IL-1β，作为溃疡性结肠炎的前 3 个枢纽基因。本研究的发现仍有待验证，但可能有助于进一步了解溃疡性结肠炎的发病机制。
