Establishment of a comparative transcriptomics database of coronavirus infected animal models
Received:November 18, 2021  
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DOI:10. 3969 / j.issn.1005-4847. 2022. 01. 012
KeyWord:coronavirus; database; SARS-CoV-2; animal model; gene expression; comparative analysis
吴玥 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
向志光 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
高苒 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
孔琪 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
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       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.
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