Fig. 4
From: Single-cell RNA reveals a tumorigenic microenvironment in the interface zone of human breast tumors
Stem cell clusters. a tSNE plots of 20,810 stem cells, color by relevant clusters (left) or sample type (right). b Pseudotime trajectory of stem cells state inferred by Monocle and characterized by subcluster (top to bottom): pseudotime characterized by a gradient from dark to light blue, pseudotime trajectory of MSCs, PSCs and progenitor cells. MSCs, Mesenchymal stem cells; PSCs, pluripotent stem cells. c Bubble plots displaying expressions of specific genes in MSCs (clusters 1 and 6), PSCs (clusters 3 and 5) and progenitor cells (clusters 0, 2, 4, 7, 8, 9, 10, 11 and 12). d Boxplots showing signature score of marker genes. The signature score is calculated by the average expression of log2(TPM + 1) of each gene in top 10 marker genes for MSCs (cluster 1 or 6) from breast cancer tissues (TCGA datasets, n = 1085) and normal breast tissues (TCGA and GTEx datasets, n = 291), **p < 0.01. e Heatmap of score differences of selected pathway activity of each cell by GSVA