New tool offers detailed data-driven treatment approach to help scientists better understand COVID-19

It is called PAGER-CoV, and it promises to be an important tool in finding treatments for COVID-19. Simply put, PAGER-CoV is a database full of nearly 12,000 (so far) pieces of genetic information on the SARS-CoV-2 virus, information that researchers can and use by doctors to make treatments against the disease.

PAGER-CoV is an extension of PAGER, a database of gene sets created by Jake Chen, Ph.D., professor in the Department of Genetics at the University of Alabama at Birmingham and associate director of the Institute of Informatics in UAB School of Medicine. Chen created PAGER 10 years ago while at Indiana University. As the pandemic spread in early 2020, Chen and his UAB colleagues created a similar system, PAGER-CoV, in response.

The database contains 11,835 PAGs, which stands pathletics, annotated gene lists and gene signatures.

Paths are the roadmap that describes how genes are turned on and off and how they establish links with each other.

Annotated gene lists are empirical information that researchers gather from experiments or literature. Gene lists help researchers understand how a particular cell type behaves under different conditions.

Gene signature is a specific pattern of intracellular gene expression from one or a group of genes, providing information about the activity of these genes in the cell.

“SARS-CoV-2 is a new virus, and we didn’t know much about its action back in the summer of 2020,” Chen said. “The aim here is to gather all this information together into a searchable database so that researchers can better understand how the virus’s genes behave or perform under different conditions. biochemical, such as solid COVID-19 or long-acting COVID-19 patients. . “

Chen states that SARS-CoV-2 has 15 genes, with very little information on how these genes affect human cells.

“We need to understand the differences in people dying from COVID-19 versus the one who has only a small case of the disease,” he said. “This is a detailed treatment method, using the database to organize everything we have learned about the virus so that the information can be used in an effective way.”

Chen says the downstream effects of coronavirus are not fully understood. Better understanding could lead to therapeutic treatment based on gene behavior.

“We need to know how the virus proteins interact with human cells, and we need to know what we can do about it,” he said. There is a lack of governments that bring the right treatment with the right person. Detailed data-driven therapy is what will help physicians understand this work with COVID-19. “

Chen and colleagues ’paper on the work of PAGER-CoV was published in January in Nucleic Acids Research. The team reviewed the medical literature for all articles dealing with the SARS-CoV-2 virus. They then used data science tools to perform complete data processing and data integration. Advanced computers have been used to establish quality measures and improve PAG-to-PAG relationships.

Chen states that users can scan the database with any human gene or PAG of interest, drill down to their database entry, and navigate to other related PAGs through either mutual relationships. PAG-to-PAG membership or PAG-to-PAG management relationships. To date, 19,996,993 PAG-to-PAG relationships are stored in the database.

“Our mission is to provide a resource that researchers using genomic analyzes of COVID-19 can use,” Chen said. “There’s a lot of information here, organized in a way that we hope will invigorate new insights and deliver meaningful results.”

PAGER-CoV will grow as new information becomes available and added to the database. Chen urges researchers around the world to take advantage of the portal and participate in this community-based information therapy effort.

PAGER-CoV is freely available to the public without registration or login requirements (http://discovery.informatics.uab.edu/PAGER-CoV/). The data available for download is based on the agreement to name this work while using the data from the PAGER-CoV website.