Powerful gene network enrichment analysis and its application to severe COVID-19 gene network. (PubMed, Brief Bioinform)
PGNEA successfully identified viral infection-related pathways enriched in severe COVID-19 gene networks, including those linked to "COVID-19," "HIV-1 infection," "Hepatitis B," "Influenza A," "Measles," and "Kaposi sarcoma-associated herpesvirus infection." Notably, key molecular markers such as PIK3, NF-B family members, FOXA, JUN, and CXCL8 were identified, with strong and consistent molecular interplays between CXCL8 and NFKBIA. These findings underscore the potential of PGNEA as an efficient tool for identifying biologically meaningful pathways and network-level mechanisms associated with various phenotypes, including severe viral infections.