Fig. 2
Transcriptomic profiles reveal that TGF-β signaling is negatively correlated with osteoblast activity. a Uniform manifold approximation and projection (UMAP) plot of all isolated regions, colored by group. b Heatmap showing the average expression of the top 20 up- and downregulated genes compared to D35. c Boxplots of osteogenesis and Wnt signaling inhibitor gene expression. Box = IQR; line = median; whisker = 1.5 × IQR. The Wilcoxon rank-sum test is used for statistics. d Violin plots of osteoblast marker gene set scores based on gene set variation analysis (GSVA). Each point = single region; Wilcoxon rank-sum test was used for statistics. e Bar plots of normalized enrichment scores of significant pathways identified by gene set enrichment analysis (GSEA). Color represents gene ratio with each pathway, representing the proportion of genes detected in the dataset relative to the total number of genes in each canonical gene set. f Violin plots of TGF-β signaling activity scores derived from GSVA. Each data point represents an individual region. The Wilcoxon rank-sum test was used for statistics. g Scatter plot showing a negative correlation between TGF-β signaling activity and osteoblast marker scores. Pearson correlation coefficient (r) and P-value are calculated across regions. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.000 1; ns not significant
