Hu Zong-Ren, Zheng Wen-Jiang, Yan Qian, Hu Wei-Wei, Sun Xiao-Sheng
School of Basic Medical Science of Guangzhou University of Chinese Medicine Guangzhou 510006, China.
the First Clinical Medical College of Guangzhou University of Chinese Medicine Guangzhou 510405, China.
Zhongguo Zhong Yao Za Zhi. 2020 Apr;45(7):1684-1690. doi: 10.19540/j.cnki.cjcmm.20191030.401.
The aim of this paper was to analyze the microarray data between ulcerative colitis(UC) patients and healthy people by bioinformatics technology, screen the differentially expressed genes of UC, and predict the potential Chinese medicines for UC. The GSE36807 gene expression profile was downloaded from the gene expression database(GEO) and the differentially expressed(both up-regulated and down-regulated) genes(DEGs) were analyzed by using R language software. The core genes in the DEGs were obtained by using String database, Cytoscape software and its plug-in analysis, and the gene ontology(GO) and Kyoto encyclopedia of genes and genomes(KEGG) were used to analyze the core genes. Moreover, the core genes and the medical ontology information retrieval platform(Coremine Medical) were mapped to each other to screen the traditional Chinese medicines and its active ingredients for treating UC. A total of 648 DEGs were screened, including 397 up-regulated genes and 251 down-regulated genes. Up-regulation of DEGs yielded 15 core genes including CXCL8, IL1 B, MMP9, CXCL1, CXCL10, CXCL9, CXCL2, CXCL5, TIMP1, CXCL11, STAT1,LCN2, IL1 RN, MMP1 and IDO1. Their biological processes and pathways were mainly enriched in interleukins, chemokine ligands and cytokines, chemokine-mediated signaling pathways, and were closely related to inflammatory responses, defense responses, cell chemotaxis, secretory granules, IL17 signaling pathways, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and TNF signaling pathway. Potential Chinese medicines for the treatment of UC include Curcumae Longae Rhizoma, Coptidis Rhizoma, Scutellariae Radix, Dendrobii Caulis, Sanguisorbae Radix, Phellodendri Chinensis Cortex, Bletillae Rhizoma and Atractylodis Rhizoma. The analysis of DEGs and core genes could promote our understanding on pathogenesis of UC. This study provides potential gene targets and research ideas for the development of new drugs of Chinese medicine intervention for UC.
本文旨在通过生物信息学技术分析溃疡性结肠炎（UC）患者与健康人之间的基因芯片数据，筛选UC的差异表达基因，并预测治疗UC的潜在中药。从基因表达数据库（GEO）下载GSE36807基因表达谱，使用R语言软件分析差异表达（上调和下调）基因（DEGs）。通过String数据库、Cytoscape软件及其插件分析获得DEGs中的核心基因，并使用基因本体论（GO）和京都基因与基因组百科全书（KEGG）对核心基因进行分析。此外，将核心基因与医学本体信息检索平台（Coremine Medical）相互映射，以筛选治疗UC的中药及其活性成分。共筛选出648个DEGs，其中上调基因397个，下调基因251个。上调的DEGs产生了15个核心基因，包括CXCL8、IL1B、MMP9、CXCL1、CXCL10、CXCL9、CXCL2、CXCL5、TIMP1、CXCL11、STAT1、LCN2、IL1RN、MMP1和IDO1。它们的生物学过程和途径主要富集在白细胞介素、趋化因子配体和细胞因子、趋化因子介导的信号通路中，并且与炎症反应、防御反应、细胞趋化性、分泌颗粒、IL17信号通路、Toll样受体信号通路、NOD样受体信号通路和TNF信号通路密切相关。治疗UC的潜在中药包括莪术、黄连、黄芩、石斛、地榆、黄柏、白及和苍术。对DEGs和核心基因的分析有助于我们了解UC的发病机制。本研究为开发中药干预UC的新药提供了潜在的基因靶点和研究思路。
