Summary of the number of differentially active pathways in the active infection group of the COVID monkey data set, by all four tested methods
| Cell type | Pathway status | SiPSiC | AUCell | ssGSEA | VAM | Overlap |
|---|---|---|---|---|---|---|
| Alveolar | Upregulated | 31 | 30 | 34 | 28 | 24 |
| Downregulated | 12 | 9 | 8 | 10 | 4 | |
| Skipped | 0 | 4 | 0 | 0 | 0 | |
| Missed | 0 | 4 | 1 | 3 | — | |
| B cells | Upregulated | 1 | 0 | 0 | 0 | 0 |
| Downregulated | 0 | 0 | 0 | 0 | 0 | |
| Skipped | 0 | 19 | 0 | 0 | 0 | |
| Missed | 0 | 0 | 0 | 0 | — | |
| T cells | Upregulated | 1 | 0 | 1 | 3 | 0 |
| Downregulated | 0 | 0 | 0 | 0 | 0 | |
| Skipped | 0 | 24 | 0 | 0 | 0 | |
| Missed | 0 | 0 | 0 | 0 | — |
[i] The overlap column shows the number of pathways found as differentially active by all methods. Skipped pathways are pathways for which AUCell could not calculate scores, and missed pathways are cases in which the relevant method failed to detect differential activity of a pathway detected by all other methods. For the analysis of all 50 hallmark pathways, see Supplemental Table S2.