Abstract

PAGER-CoV (http://discovery.informatics.uab.edu/PAGER-CoV/) is a new web-based database that can help biomedical researchers interpret coronavirus-related functional genomic study results in the context of curated knowledge of host viral infection, inflammatory response, organ damage, and tissue repair. The new database consists of 11 835 PAGs (Pathways, Annotated gene-lists, or Gene signatures) from 33 public data sources. Through the web user interface, users can search by a query gene or a query term and retrieve significantly matched PAGs with all the curated information. Users can navigate from a PAG of interest to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships, totaling 19 996 993. Users can also retrieve enriched PAGs from an input list of COVID-19 functional study result genes, customize the search data sources, and export all results for subsequent offline data analysis. In a case study, we performed a gene set enrichment analysis (GSEA) of a COVID-19 RNA-seq data set from the Gene Expression Omnibus database. Compared with the results using the standard PAGER database, PAGER-CoV allows for more sensitive matching of known immune-related gene signatures. We expect PAGER-CoV to be invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients.

中文翻译：

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PAGER-CoV：用于冠状病毒疾病研究的途径，注释的基因清单和基因签名的全面集合

摘要

PAGER-CoV（http://discovery.informatics.uab.edu/PAGER-CoV/）是一个新的基于Web的数据库，可以帮助生物医学研究人员在正确掌握宿主病毒的背景下解释冠状病毒相关的功能基因组研究结果感染，炎症反应，器官损伤和组织修复。新数据库由11 835 PAG组成来自33个公共数据源的（路径，带注释的基因列表或基因签名）。通过Web用户界面，用户可以按查询基因或查询词进行搜索，并检索与所有策划信息完全匹配的PAG。用户可以通过共享的PAG到PAG共同成员关系或PAG到PAG监管关系从感兴趣的PAG导航到其他相关的PAG，总计19 996993。用户还可以从COVID的输入列表中检索丰富的PAG。 -19个功能研究结果基因，定制搜索数据源，并导出所有结果以用于后续脱机数据分析。在一个案例研究中，我们对来自Gene Expression Omnibus数据库的COVID-19 RNA-seq数据集进行了基因集富集分析（GSEA）。与使用标准PAGER数据库的结果相比，PAGER-CoV可以更敏感地匹配已知的免疫相关基因标记。我们希望PAGER-CoV对于生物医学研究人员发现分子生物学机制和量身定制的疗法来治疗COVID-19患者具有无价的价值。