PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies

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.

Aviator: a web service for monitoring the availability of web services

“…We selected one of the publications presenting PAGER-CoV ( 30 ). This tool uses google-analytics and was permanently online since it has been published.…”

Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19

“…Nevertheless, further (in vitro and in vivo) validations are warranted to test the hypotheses arising from the current study. Recently there have been several studies and databases reporting COVID-19-specific databases, 33,[50][51][52] which can be either used to compile additional consensus gene sets or for further functional characterization of the modules discovered in the current study.…”

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

“…In a similar vein, DockCoV2 ( 9 ) contains in silico docking results for already approved drugs against putative drug targets in the SARS-Cov-2 proteome. Finally, recognising the therapeutic importance of an understanding of the host response, PAGER-CoV ( 10 ) covers pathways and gene lists relating to the viral infection and its consequences.…”