福建农业学报2025，Vol.40Issue(3)：253-261,9.DOI:10.19303/j.issn.1008-0384.2025.03.005
基于生物信息学筛选小鹅瘟差异表达基因及潜在治疗中药预测
Bioinformatics of Goose Parvovirus DEGs and Potential Traditional Chinese Medicines for Preventing and Treating Gosling Plague
摘要
Abstract
[Objective]Key pathogenic genes and signaling pathways of gosling plague(GP)were analyzed on the bioinformatics databases to screen traditional Chinese medicines(TCMs)for disease intervention potential.[Method]GP-related differentially expressed genes(DEGs)were collected from GeneCards and standardized using the Uniprot database.The intestinal inflammation dataset GSE14841 and malnutrition dataset GSE43698 from Gene Expression Omnibus(GEO)were extracted and combined.DEGs of GP were screened using the Limma package in R language.DAVID was employed for the GO and KEGG enrichment analyses on the DEGs.STRING was applied to construct the protein-protein interaction network(PPI),and Cytoscape and its plugins to select relevant genes in the sub-network.The genes were then mapped with Coremine Medical to search for potential TCMs in treating GP.[Result]The 58 selected DEGs were mainly associated with the biological processes such as the recognition of viral proteins by the host cell membrane receptors and the activities of cytoplasmic hydrolases and transferases.They were in the actin cytoskeleton(AC),cytosolic DNA-sensing and STING(cGAS-STING),mitogen-activated protein kinase(MARK)and toll-like receptor(TLR)signaling pathways.The PPI identified top 10 key genes by the Degree to be the interferon induced with helicase C domain 3(IFIH3)and those with helicase C domain 1(IFIH1),mitochondrial antiviral signaling protein(MAVS),C-C motif chemokine ligand 5(CCL5),toll-like receptor 4(TLR4),nuclear factor-kappa B(NF-κB),ras-related C3 botulinum toxin substrate 2(RAC2),toll-like receptor 9(TLR9),early growth response 1(EGR1),and erb-B2 receptor tyrosine kinase 3(ERBB3).TLR4,TLR9,NF-κB,and ERBB3 were the 4 genes in inflammatory response to GP.Fifty TCMs in 4 therapeutic classes of Chines medicines,i.e.,heat-alleviating and detoxifying,tonics for health deficiencies,exterior-releasing,and anti-diarrheal agent,appeared to have potential in deterring or combating GP.[Conclusion]The bioinformatic analysis identified 4 key genes related to GP and 50 TCMs of potential for treating the disease.These clues could be of value in the search for natural agents to prevent and/or treat GP in geese.关键词
小鹅瘟/鹅细小病毒/中药预测/虚拟筛选/生物信息学Key words
gosling plague/goose parvovirus/traditional Chinese medicines/virtual screening/bioinformatics分类
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王劭,孙雪岩,张烨淳,袁孝武,徐见光,邝启红,陈少莺,陈仕龙,俞道进..基于生物信息学筛选小鹅瘟差异表达基因及潜在治疗中药预测[J].福建农业学报,2025,40(3):253-261,9.基金项目
国家自然科学基金项目(31272606、31402236) （31272606、31402236）
