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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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1094","type":"journal-article","created":{"date-parts":[[2020,10,27]],"date-time":"2020-10-27T12:47:48Z","timestamp":1603802868000},"page":"D589-D599","source":"Crossref","is-referenced-by-count":10,"title":["PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies"],"prefix":"10.1093","volume":"49","author":[{"given":"Zongliang","family":"Yue","sequence":"first","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Zhang","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2384-4244","authenticated-orcid":false,"given":"Clark","family":"Xu","sequence":"additional","affiliation":[{"name":"University of Wisconsin-Madison School of Medicine and Public Health, Institute of Clinical and Translational Research, Madison, WI 53705-2221, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sunny","family":"Khurana","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nishant","family":"Batra","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Son\u00a0Do\u00a0Hai","family":"Dang","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James J","family":"Cimino","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8829-7504","authenticated-orcid":false,"given":"Jake Y","family":"Chen","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35223, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,27]]},"reference":[{"key":"2021010313123827800_B1","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/s41586-020-2355-0","article-title":"Viral and host factors related to the clinical outcome of COVID-19","volume":"583","author":"Zhang","year":"2020","journal-title":"Nature"},{"key":"2021010313123827800_B2","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/s41586-020-2332-7","article-title":"Proteomics of SARS-CoV-2-infected host cells reveals therapy targets","volume":"583","author":"Bojkova","year":"2020","journal-title":"Nature"},{"key":"2021010313123827800_B3","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/cvr\/cvaa191","article-title":"Single-cell analysis of SARS-CoV-2 receptor ACE2 and spike protein priming expression of proteases in the human heart","volume":"116","author":"Liu","year":"2020","journal-title":"Cardiovasc. 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