Differential Expression and Enrichment Analysis
The raw counts from the SARS-coV-2 transcriptomic profiles were
subjected to differential expression analysis by DESEq2 v1.26.025. Subsequently the genes were pre-ranked using the
p-values from DESeq2 analysis and subjected to pre-ranked gene set
enrichment analysis (GSEA) 26. Gene sets with FDR
<0.05 were considered to be statistically significant and were
visualized using EnrichmentMap plugin 27 of Cytoscape28. For drug signatures from iLINCS, differentially
expressed genes with p<0.05 were considered to be
statistically significant. Enrichment of kinase perturbation was carried
out using Enrichr 29.