Fig. 2: Comparison of the transcriptional response to HCMV infection in different cell lines.

a Dot plot visualization of over-represented selected gene ontology (GO) terms in RPTECs, ARPE-19 and HFFs. Over-representation analyses were performed using Metascape, as reported in the Materials and Methods section. Each dot on the plot represents a GO term, with the color indicating the -Log10 (p value) for the enrichment, and the size representing the number of genes enriched in the gene set. b Heatmap showing unsupervised hierarchical clustering of DEGs enriched in the GO term “Inflammatory response” in HCMV-infected vs. mock-infected cells based on Metascape analysis. For each gene, log2 fold change (log2FC) and false rate discovery (FDR) between HCMV- and mock-infected cells are reported for each cell line, separated by semicolon. When TPM < 1, “Not_expr” string is indicated. c Gene set enrichment analysis (GSEA) was conducted to investigate the enrichment of hallmark gene sets from MSigDB Collection in HCMV-infected RPTECs vs. mock-infected controls. Positive normalized enrichment score (NES) indicate enrichment (green bars), whereas negative NES indicate downregulation in virus-infected cells (red bars). Hallmarks with a |NES | > 1 and FDR q-value < 0.05 are considered statistically significant and are shown. d GSEA of the comparison between HCMV-infected and mock-infected RPTECs showing the enrichment of hallmark pathways of allograft rejection. The green curve in the GSEA plot represents the enrichment score curve. Genes on the far left (red) correlate with HCMV-infected cells, whereas genes on the far right (blue) correlate with mock-infected cells. The vertical black lines indicate the position of each gene in the gene set analyzed. NES, false discover rate (FDR), and nominal P-value are shown for this hallmark.