Fig. 3

Pseudo-time cell trajectories depicting the alterations in epithelial cells during nodular formation using scRNA-seq. A Pseudo-time cell trajectory of LE2 and BE5 cells colored by epithelial cell subtypes (Epi), state, and pseudo-time. B Heatmap showing the selected DEGs (q value < 1e-04) which was clustered into three profiles as well as the significant enriched Hallmark pathways for each cluster (p value < 0.05; FDR < 0.05). C Pseudo-time cell trajectory of LE2 and BE5 cells colored by the expression levels of FOS and JUN and the scores of Hypoxia and EMT signaling pathways. D Pseudo-time cell trajectory of BE5, BE6, and BE7 cells colored by epithelial cell subgroups (Epi), state, pseudo-time, and the expression levels of FOS and JUN. E Heatmap showing the selected DEGs (q value < 1e-04) which was clustered into six profiles as well as the significant enriched Hallmark pathways for each cluster (p value < 0.05; FDR < 0.05). F Pseudo-time cell trajectory of BE5, BE6, and BE7 cells colored by the scores of Hypoxia and EMT signaling pathways (up); Bar plot illustrating the scores of Hypoxia and EMT signaling pathways among root, fate 1, and fate 2 cells (down). G Dot plots of dynamic expression of FOS and JUN along two cell fates. Hypoxia and EMT gene sets were scored using AddModuleScore method. The p values of the comparison between two variables were determined using a two-sided Wilcoxon test. Error bar represented standard error. “****”, p value < 0.0001