Fig. 6: Myc;Ptenfl subtypes show distinct cell types and cluster gene enrichments. | Nature Communications

Fig. 6: Myc;Ptenfl subtypes show distinct cell types and cluster gene enrichments.

From: MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

Fig. 6

A UMAP showing scRNA-seq data from Myc;Ptenfl model. Color-coded by either lineage or unsupervised cluster. UMAP was computed on 50 iNMF factors. Lineage was manually assigned using canonical cell type markers (Source Data) for unsupervised clusters. Unsupervised clusters were identified using the Leiden algorithm to the same 50 iNMF factors (Resolution = 0.45, optimized for silhouette width, Supplemental Fig. S13B). B Bar-plot is showing the relative fraction of each tumor assigned to each cell lineage. Stromal-Rich (SR) and Stromal-Poor (SP) subtypes were based on initial two-class histology assigned by a pathologist and cell type fractions, which were further divided into Stromal-Rich-Immune-Rich (SR-IR) and Stromal-Rich-Immune-Poor (SR-IP). C Relative abundance of cell type clusters for each Myc;Ptenfl tumor subtype. Mean frequency is the arithmetic mean across all tumors within that subtype, and error bars represent SEM. D UMAP visualizations of individual lineages. UMAPs and clustering were computed using the same 50 factors as global analysis (Fig. 6A, Supplemental Fig. S13C). E Heatmap showing the top 10 uniquely upregulated genes for each epithelial cluster (min.pct = 0.1, avg_log2FC > 0.5, Bonferroni corrected p ≦ 0.05). F Enrichment maps showing the top 30 enriched ontologies for each epithelial cluster visualized as a network. The size of the point indicates the number of genes within the ontology that were uniquely upregulated in that cluster. Edges connect any ontologies with a Jaccard similarity greater than 0.2 and edge width scaled to Jaccard similarity. G Heatmap showing the top 10 uniquely upregulated genes for each fibroblast cluster (min.pct = 0.1, avg_log2FC > 0.5, Bonferroni corrected p ≦ 0.05). H Enrichment maps showing the top 30 enriched ontologies for each fibroblast cluster visualized as a network. The size of the point indicates the number of genes within the ontology that were uniquely upregulated in that cluster. Edges connect any ontologies with a Jaccard similarity greater than 0.2 and edge width scaled to Jaccard similarity.

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