Fig. 5

The time-course scRNA-seq data analysis for the NK cell response to SARS-COV-2 infection. A The experimental design of SARS-COV-2 infection samples from PBMC. The scRNA-seq data were assayed by 10X Genomics Chromium protocols, consisting of 5 stages, i.e., stage I (4–8 days), stage II (10–13 days), stage III (19–24 days), stage IV (28–34 days), and stage V (110–123 days). B The UMAP demonstrates cell alignment from different stages. These scRNA-seq datasets display strong batch effects over heterogeneous samples (iLISI = 0.10, left panel). The cells are well-aligned after performing integrative analysis using scMerge (iLISI = 0.36, right panel). C The quantile–quantile (QQ) plot shows the type I error control under the permutation strategy. The well-calibrated p-values will be expected laid on the diagonal line. The p-values produced by Mixed TDEseq (plum), Mixed TDEseq coupled with scMerge (purple), and tradeSeq (green) are reasonably well-calibrated, while those from ImpulseDE2 (blue) are overly conservative, and those from edgeR (dark green) and DESeq2 (brown) are inflated. D The power comparison of temporal expression gene detection across a range of FDR cutoffs. The TDEseq methods were highlighted using solid lines, while other methods were represented by dashed lines in the plots. TDEseq coupled with scMerge is more powerful in identifying more temporal expression genes than other comparative methods. E The heatmap demonstrates the pattern-specific temporal expression genes that were identified by Mixed TDEseq coupled with scMerge. Gene expression levels were log-transformed and then standardized using z-scores for visualization. The top-ranked temporal expression genes identified by Mixed TDEseq coupled with scMerge show distinct four patterns. F The Venn diagram shows the overlapping of the temporally expressed genes (FDR ≤ 0.05) identified by Mixed TDEseq coupled with scMerge, tradeSeq, DESeq2, and edgeR. ImpulseDE2 was excluded because it only identified 3 temporal DE genes. Those method-specific unique genes were enriched in the number of GO terms (N_GO, BH-adjusted p-value < 0.05). The temporal expression genes detected by Mixed TDEseq coupled with scMerge enriched more GO terms. G The bubble plot demonstrates the significant GO terms enriched by pattern-specific temporal expression genes, which were identified by Mixed TDEseq coupled with scMerge. The Wilcoxon test was excluded from this comparison due to its poor performance in simulations. FDR denotes the false discovery rate