Fig. 2
The time-resolved scRNA-seq data analysis for the HCT116 cell lines after 5-AZA-CdR treatment. A The experimental design of HCT116 cell lines treated with 5-AZA-CdR. The scRNA-seq data were assayed by Well-TEMP-seq protocols, consisting of four time points, i.e., D0, D1, D2, or D3 after treatment. B The quantile–quantile (QQ) plot shows the type I error control under the null simulations with permutation strategy. The well-calibrated p-values will be expected laid on the diagonal line. The p-values produced by Linear TDEseq (orange) and tradeSeq (green) are reasonably well-calibrated, while those from ImpulseDE2 (blue) are overly conservative. C The power comparison of temporal expression gene detection across a range of FDR cutoffs. Linear TDEseq was highlighted using solid lines, while other methods were represented by dashed lines in the plots. Linear TDEseq displays the powerful performance of temporal expression gene detection. D The heatmap demonstrates the pattern-specific temporal expression genes that were identified by Linear TDEseq. Gene expression levels were log-transformed and were standardized using z-scores for visualization. The top-ranked temporal expression genes identified by Linear TDEseq show distinct four patterns. E The Venn diagram shows the overlapping of the temporally expressed genes (FDR ≤ 0.05) identified by Linear TDEseq, tradeSeq, or ImpulseDE2. Those method-specific unique genes were enriched in the number of GO terms (NGO, BH-adjusted p-value < 0.05). The temporal expression genes detected by Linear TDEseq were enriched with a greater number of GO terms. F The UMAP shows two temporal expression genes, i.e., DKK1 and IFITM3, which were identified by Linear TDEseq but not by tradeSeq. G The bubble plot demonstrates the significant GO terms enriched by pattern-specific temporal expression genes, which were identified by Linear TDEseq. The peak-specific temporal expression genes enriched more significant GO terms. The Wilcoxon test was excluded from this comparison due to its poor performance in simulations. DESeq2 and edgeR were excluded from this comparison due to only one sample at each time point. FDR denotes the false discovery rate