Fig. 5

GSEA analysis of the Reactome pathways of proteins with altered phosphorylation at the early stages of infection. a NES plotted against the significance of Reactome pathways generated by GSEA at 1 h, 2 h and 3 h after infection. The FDR q-value of a pathway is plotted with a red box, while the corresponding p-value is plotted with a black box. b Heat map of the NESs of the Reactome pathways resulting from the GSEA analysis. The four columns corresponds to the 1 h and 3 h time points of the iAT2 cell (Hekman et al. 2020) and the 2 h and 4 h time points of Vero E6 cells (Bouhaddou et al. 2020) after the infection by SARS-CoV-2. The numbers in small rectangles on the heat map indicate the number of proteins in the CES that contain phosphosites upregulated by SARS-CoV-2 infection and inhibited by CIGB-300 (Perera et al. 2020). c Venn diagram for sets of phosphorylation sites of proteins in the CES for “mRNA Splicing/Processing of capped intron containing pre-mRNA” Reactome pathways at 1 h, 2 h and 3 h time points or that were inhibited by the action of CIGB-300 according to Perera et al. (2020). The sites upregulated in one of the three time points and inhibited by CIGB-300 are listed. d PPI—Networks of proteins in “mRNA Splicing” CES for 1 h, 2 h and 3 h post infection time points. Shown in green are the nodes with the highest degrees; at the center, in yellow, are the nodes representing proteins found in all sub-networks. e Profile of the Running ES Score for “mRNA Splicing” gene sets at 1 h, 2 h and 3 h post infection. The middle panel of the plots shows the positions of the members of the gene set on the ranked list. The bottom panel shows the value of the ranking metric (phosphorylation changes) in a descending order