Fig. 5: Early and late responding human genes to SARS-CoV-2 infection.

a Differentially expressed genes (DEGs) identified from RPF-seq data are shown for each time point. From 0 to 36 hpi, RPF-seq levels of human genes were compared with those of uninfected condition. Log₂(expression fold change) (x-axis) and statistical significance (y-axis; −log₁₀-scale FDR-corrected q value) of each gene are displayed (see “Methods”). For a subset of DEGs with q < 0.01, highly upregulated and downregulated DEGs with |log₂(expression fold change)| ≥ 2.0 are indicated in red and blue, respectively, and moderately upregulated and downregulated DEGs with |log₂(expression fold change)| < 2.0 are indicated in pink and light blue, respectively. b Hierarchical clustering of the DEGs displayed in a. The genes identified as DEGs at least for one time point were clustered with respect to their temporal expression patterns (see “Methods”). Upregulation and downregulation in comparison to the uninfected condition is indicated in red and blue, respectively. c Temporal expression changes of the identified DEGs color-coded for the five clusters determined in b (left). Overall expression changes for each cluster were also depicted by mean log₂(expression fold changes) (right). The light-colored shades for each line indicate the standard deviations, and the gray lines represent the expression changes of individual DEGs (left). For the DEGs included in each cluster determined in b, Gene Ontology (GO) enrichment analysis were performed and GO terms associated with early (d, e) and late (f, g) responding clusters in response to the viral infection are shown. For each cluster, top five GO terms chosen based on statistical significance and their temporal expression patterns are displayed (see “Methods”).