SARS-CoV-2 Gene Database Offers Precision Medicine Approach for Tailoring COVID-19 Treatments

A database packed with nearly 12,000 pieces of genetic information on the SARS-CoV-2 virus promises to be an important tool in finding therapies for COVID-19.

The database, called PAGER-CoV, developed by scientists at the University of Alabama at Birmingham (Birmingham, AL, USA) is an extension of PAGER, a database of gene sets created some 10 years ago. The database includes 11,835 PAGs, which stands for pathways, annotated gene lists and gene signatures. Pathways are the roadmap that describes how genes are turned on and off and how they establish connections with each other.

Annotated gene lists are empirical information that researchers collect from experiments or literature. Gene lists help researchers understand how a certain cell type behaves under different conditions. A gene signature is a unique pattern of gene expression within a cell from a single or group of genes, providing information about the activity of those genes in the cell. According to the scientists, SARS-CoV-2 has 15 genes, with scant information on how these genes affect human cells. The downstream effects of coronavirus are not well understood, and a better understanding could lead to tailored therapeutics based on gene behavior.

The scientists searched the medical literature for all articles dealing with the SARS-CoV-2 virus. They then employed data science tools to do comprehensive data processing and data integration. Super computers were used to establish quality measures and develop PAG-to-PAG relationships. Users can search the database with any human gene or a PAG of interest, drill down to their database entry, and navigate to other related PAGs through either shared PAG-to-PAG co-membership relationships or PAG-to-PAG regulatory relationships. To date, there are 19,996,993 PAG-to-PAG relationships stored in the database. PAGER-CoV is freely available to the public without registration or login requirements and will grow as new information is available and added to the database.

“The goal here is to gather all this information together in a searchable database so that researchers can gain a better understanding of how the virus’s genes behave or perform under various biophysical conditions, such as severe COVID-19 or long-haul COVID-19 patients,” said Jake Chen, Ph.D., professor in the Department of Genetics at the University of Alabama at Birmingham and associate director of the Informatics Institute in the UAB School of Medicine. “We need to know how the virus proteins are interacting with human cells, and we need to know what we can do about it. There is no shortage of possible therapeutics. There is a shortage of regimens that will pair the right therapeutic with the right person. Precision data-driven medicine is what this work will help COVID-19 physicians understand.”

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University of Alabama at Birmingham