Figure 3
Pathways associated with SARS-CoV-2 infection in lung cells in vitro. (a) Significance of enrichment (by one-sided Fisher’s exact test) for wikiPathway18 gene sets within the respective sets of genes up-regulated with SARS-CoV-2 infection according to cell line (from Fig. 2b,c). Signatures represented are: up-regulated in all three cell lines examined (NHBE, A549, and Calu-3), A549-specific up-regulation, Calu-3-specific up-regulation, and up-regulated specifically in both A549 and Calu-3. Pathways represented were significant (FDR < 1%39) within at least one of the above gene sets. (b) Selected significantly enriched Gene Ontology (GO) terms, involving the gene sets described in part a. Enrichment p values by one-sided Fisher’s exact test. (c) Pathway diagram representing type II interferon signaling (from wikiPathways), with differential expression patterns in response to SARS-CoV-2 infection in each of the three cell lines represented (left, NHBE; middle, A549; right, Calu-3). Red, high in SARS-CoV-2-infected group versus control. p values by t test using log-transformed values. (d) Similar to part c, but for wikiPathway “Cytokines and inflammatory response”. See also Supplementary Data S2 and Supplementary Data S3 (which files provide the numbers of genes involved with each pathway or annotation term).
