Fig. 1
The PBMC proteome of critically ill COVID-19 patients. A PCA, UMAP and t-SNE plots of the proteome data showing segregation of the COVID-19 (COV) and ICU (COV-) samples away from the healthy controls (HC). B A bar graph showing the number of proteins with significantly increased (red) or decreased (blue) expression between the patient and HC groups. Proteins with the log2 difference > 1 and p < 0.1 between the two groups shown were considered significant. The bar graph is a summary of the differentially expressed proteins between the COVID-19+ day 1, 7 or 10 samples and the HC, the COV- ICU samples vs. the HC, or the COV_D1 vs. ICU. C A volcano plot of the proteins identified in the COV_D1 samples. The significantly differentially expressed proteins (DEPs) are highlighted in red (i.e., increased expression over HC) or blue (i.e., decreased expression over HC). D, E. The enriched functions in the COV groups (D) or HC (E) identified by Metascape analysis based on the corresponding DEPs. The color of the circle denotes the p value (-logP) whereas the size of the circle is proportional to the number of proteins involved in each term. The largest number of proteins (corresponding to the largest circle) is 42. The full list of 3047 identified proteins was used as the background dataset for enrichment. Enrichment terms with -logP > 3 are shown. F Changes in cell-type signature proteins between the patient and the HC groups. P < 0.1 between the HC and at least one of the patient groups (student’s t-test)