冠状病毒感染动物模型比较转录组学数据库的建立  

Establishment of a comparative transcriptomics database of coronavirus infected animal models

作　　者：吴玥 向志光 高苒 孔琪 WU Yue;XIANG Zhiguang;GAO Ran;KONG Qi(Institute of Laboratory Animal Sciences,Chinese Academy of Medical Sciences(CAMS)&Comparative Medicine Center,Peking Union Medical Collage(PUMC),NHC Key Laboratory of Human Disease Comparative Medicine,Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases,Key Laboratory of Human Diseases Animal Model,State Administration of Traditional Chinese Medicine,Beijing 100021,China)

机构地区：[1]中国医学科学院医学实验动物研究所,北京协和医学院比较医学中心,国家卫生健康委员会人类疾病比较医学重点实验室,新发再发传染病动物模型研究北京市重点实验室,北京市人类重大疾病实验动物模型工程技术研究中心,国家中医药管理局人类疾病动物模型三级实验室,北京100021

出　　处：《中国实验动物学报》2022年第1期92-99,共8页Acta Laboratorium Animalis Scientia Sinica

基　　金：北京市自然科学基金资助项目(M21027);传染病重大专项(2017ZX10304402-001)。

摘　　要：目的构建冠状病毒感染动物模型比较转录组学数据库,从基因表达水平比较冠状病毒感染人和动物模型后的异同,为动物实验与临床研究提供数据支撑。方法从GEO、ArrayExpress等数据库中下载冠状病毒(以SARS-CoV、SARS-CoV-2、MERS-CoV为主)感染动物模型与人的转录组数据,对测序数据进行质控、标准化、去除批次效应,分析不同病毒株在感染不同物种、细胞或组织后所引起的基因表达变化,构建基于Django网络应用框架的数据库,建立检索界面,提供数据分析与可视化展示功能。结果本研究系统性整理了43套测序数据集,建立了冠状病毒感染动物模型比较转录组学数据库。数据库包含3种冠状病毒、4个物种、14种组织/细胞、2373个样本。数据库展示不同基因在不同物种、不同病毒株、不同感染时间、不同滴度、不同细胞或组织中的表达差异。同时嵌入生物信息学分析工具可挖掘基因表达差异,富集差异基因的分子功能、信号通路,并预测对细胞的潜在影响。结论本文建立了冠状病毒感染动物模型比较转录组学数据库。可为冠状病毒感染动物模型基因表达水平研究提供数据资源和分析工具。Objective To establish a comparative transcriptomics database of coronavirus infected animal models,explain the similarities and differences between human and animal models of coronavirus infection at the gene expression level,and provide evidence-based support for animal experiments and clinical research.Methods We downloaded coronavirus(mainly severe acute respiratory syndrome coronaviru,SARS-CoV;severe acute respiratory syndrome coronavirus 2,SARS-CoV-2 and middle east respiratory syndrome coronavirus,MERS-CoV)infected animal models and human gene expression profiles from the Gene Expression Omnibus(GEO)and ArrayExpress databases,performed quality control,standardization,and removal of the batch-effect,analyzed differential gene expression of different species,cells,or tissues infected by some virus subtypes of above coronavirus,constructed a database based on the Django web application framework,established retrieval interface,data analysis and visualization tools.Results We established a comparative transcriptomics database of coronavirus infected animal models based on 43 datasets,comprising 3 coronaviruses,4 species,14 tissues/cells,and 2373 samples.The database includes gene expressions of different species,virus strains,infection times,titers,and cells/tissues.In addition,we developed bioinformatics analysis tools to enable the analysis of differential genes and to predict the enrichment of molecular functions,pathways,and effects on cells.Conclusions In this study,we established a comparative transcriptomics database of coronavirus infected animal models that provides data resources and analysis tools for the study of coronavirus infected animal models under different conditions and gene expression levels.

关 键 词：冠状病毒 数据库 SARS-CoV-2 动物模型 基因表达 比较分析 

分 类 号：Q95-33[生物学—动物学]