Bioinformatic analysis of differentially expressed genes and Chinese medicine prediction for ulcerative colitis
(2.the First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China 510405)
(3.Institute of Tropical Medicine of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China 510405)
【Abstract】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 medicinals 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 were analyzed by using R language software. The hub genes in the differentially expressed genes 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 hub genes. Moreover, the hub genes and the medical ontology information retrieval platform (Coremine Medical) were mapped to each other to screen the Chinese medicinals and its active ingredients for treating UC. A total of 648 differentially expressed genes were screened, including 397 up-regulated genes and 251 down-regulated genes. Up-regulation of differentially expressed genes yielded 15 hub genes including CXCL8, IL1 B, MMP9, CXCL1, CXCL10, CXCL9, CXCL2, CXCL5, TIMP1, CXCL11, STAT1, LCN2, IL1RN, MMP1 and IDO1. Their biological processes and pathways were mainly enriched in interleukins, chemokine ligands, and cytokine- and chemokine-mediated signaling pathways, and were closely related to inflammatory responses, defense responses, cell chemotaxis, secretory granules, IL-17 signaling pathways, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and TNF signaling pathway. Potential Chinese medicinals for the treatment of UC include Rhizoma Curcumae Longae, Rhizoma Coptidis, Radix Scutellariae, Herba Dendrobii, Radix Sanguisorbae, Cortex Phellodendri, Rhizoma Bletillae, and Rhizoma Atractylodis. The analysis of differentially expressed genes and hub genes could promote our understanding on the pathogenesis of UC. This study provides potential gene targets and research ideas for the development of new Chinese medicine in UC intervention .
【Keywords】 ulcerative colitis; differentially expressed genes; hub genes; gene ontology (GO); Kyoto encyclopedia of genes and genomes (KEGG); protein-protein interaction; Chinese medicine prediction;
(Translated by ZHAO B)
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