UAB-developed research tool to help scientists understand COVID-19
Researchers at University of Alabama at Birmingham have developed PAGER-CoV, which is a database packed with nearly 12,000 (so far) pieces of genetic information on the SARS-CoV-2 virus – information that researchers and physicians can use to tailor treatments against the disease, according to a press release from the university.
PAGER-CoV is an extension of PAGER, a database of gene sets created by Jake Chen, PhD, a 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. Chen created PAGER some 10 years ago while he was 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 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.
Chen says SARS-CoV-2 has 15 genes, with scant information on how these genes affect human cells.
Chen and colleagues’ paper on the workings of PAGER-CoV was published in January in Nucleic Acids Research. The team 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.
PAGER-CoV is freely available to the public without registration or login requirements http://discovery.informatics.uab.edu/PAGER-CoV/.
