Figure 2
Differentially expressed genes cluster into response patterns showing distinct functions. (A) Cluster analysis identified 6 robust clusters encompassing the response profiles of all 3509 differentially expressed (DE) genes. Numbers of genes per cluster are shown. Y-axis shows the mean expression of the genes at each respective time point, centered to mean zero and scaled to standard deviation one. (B) Reactome gene set enrichment analysis shows enriched pathways for 4 out of the 6 clusters. (C) Enrichment analysis by Fisher’s exact test of non-coding RNAs per cluster. Significance is shown in shades of red. Log2 odds ratios are plotted on the x-axis and indicate enrichment or depletion. Error bars indicate 0.95 confidence intervals. (D) Scaled relative protein levels (Olink) in the unstimulated condition and after 4 h of stimulation for the three independent experiments (black dots). Box colors above the dotplots indicate the cluster in which the DE genes are found. Mean, minimum and maximum relative protein levels are indicated in red. Nominal significance is indicated by asterisks (*p value < 0.05, **p value < 0.01, ***p value < 0.001 and ****p value < 0.0001).
