Fig. 3
The time-course scRNA-seq data analysis for mouse fetal liver development. A The experimental design of mouse fetal liver sample collection. The scRNA-seq data were assayed on the FACS isolated cell populations, consisting of seven liver developmental stages, i.e., E10.5, E11.5, E12.5, E13.5, E14.5, E15.5, and E17.5. B 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 Linear TDEseq (orange), Mixed TDEseq (plum), 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. The TDEseq methods were highlighted using solid lines, while other methods were represented by dashed lines in the plots. Both versions of TDEseq display 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 more GO terms. F The UMAP shows two temporal expression genes, i.e., Atf4 and Itgb1, which were uniquely identified by Linear TDEseq. G The bubble plot demonstrates the significant GO terms enriched by pattern-specific temporal expression genes, which were identified by Linear TDEseq. The recession-specific temporal expression genes enriched more significant GO terms, whereas trough-specific temporal expression genes were not enriched in any 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 or two samples at each time point. FDR denotes the false discovery rate