Figure 6

ECM subcluster profiling and intercellular communication dynamics in wildtype and ret mutant zebrafish

(A) Uniform manifold approximation and projection (UMAP) analysis of extracellular matrix (ECM) shows all 8 subclusters. UMAP atlas was separated between wildtype and ret mutant zebrafish cells.

(B) Feature dot plot representing the expression level of the top 5 transcripts (ordered by average log₂ fold change) per subcluster of ECM between wildtype and ret mutant zebrafish cells.

(C) Cluster size comparison of each ECM subcluster between wildtype and ret mutant zebrafish cells. Significantly differentially distributed subclusters are represented in orange. The significance of differences was determined by a threshold of the false discovery rate (FDR) < 0.05 and an absolute log₂ fold change >0.58. The dotted line indicated the threshold of log₂ fold change.

(D) Bar plot (top) and stacked bar plot (bottom) show the cell number contributing to each subcluster of all ECM cells in wildtype (light-blue) and ret mutant zebrafish (light-purple) samples.

(E) GSEA of hallmark gene signatures represents different functionalities of epithelium subclusters.³⁵ Blue indicates the down-regulated pathways in ret mutant zebrafish ECM subclusters, and red indicates the up-regulated pathways in ret mutant zebrafish epithelium. The significance threshold of FDR-adjusted p value (adjusted P) < 0.05 was applied. NES: Normalized enrichment score.

(F) Heatmap of differentially expressed genes, which were involved in significantly altered hallmark pathways between wildtype and ret mutant ECM subclusters. Green indicates down-regulated genes in ret mutant ECM subclusters, while pink indicates up-regulated genes in ret mutant ECM subclusters.