Fig. 4
The time-course scRNA-seq data analysis for human metastatic LUAD. A The experimental design of human lung sample collection. The scRNA-seq data were assayed by 10X Genomics Chromium protocols, consisting of 4 LUAD evaluation stages, i.e., normal, stage I (early LUAD), stage III (advanced LUAD), and stage IV (lymph node metastasis). 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) and Mixed TDEseq(plum) are reasonably well-calibrated, while those from tradeSeq (green), ImpulseDE2 (blue) edgeR (dark green), and DESeq2 (brown) are inflated. 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 Mixed TDEseq. Gene expression levels were log-transformed and were standardized using z-scores for visualization. The top-ranked temporal expression genes identified by Mixed TDEseq show distinct four patterns. E The Venn diagram shows the overlapping of the temporally expressed genes (FDR ≤ 0.05) in pairwise comparisons between Mixed TDEseq and tradeSeq, ImpulseDE2, DESeq2, and edgeR. Those method-specific unique genes were enriched in the number of GO terms (NGO, BH-adjusted p-value < 0.05). Many more GO terms were enriched in the Mixed TDEseq-unique temporal expression genes than in other methods. F The proportion of enrichment for the detected temporal expression genes. The given gene set (136 genes) was collected from ONGene [67] database. Mixed TDEseq enriched more temporal genes than other methods across a range of top-number cutoffs. G The bubble plot demonstrates the significant GO terms enriched by pattern-specific temporal expression genes, which were identified by Mixed TDEseq. The Wilcoxon test was excluded from this comparison due to its poor performance in simulations. FDR denotes the false discovery rate