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. 2023 May 27;14:3074. doi: 10.1038/s41467-023-38886-8

Fig. 3. NMF defines malignant cell states in FN RMS tumours.

Fig. 3

a Left panel: Heatmap showing the pairwise Pearson correlations between all NMF-defined transcriptional programs in FN samples. The tumour sample from which each transcriptional program was derived is shown in the colour bar. Meta-program clusters are delineated by black boxes and colouring of the dendrograms. Right panel: Scaled expression of the top 30 genes per meta-program across all FN cells (Myo = Myoblast-like, Prog = Progenitor-like and Mes = Mesenchymal-like). The corresponding tumour sample and inferred cell cycle phase of each cell are displayed in the top annotation track. Representative genes from each meta-program are labelled. b Scatterplot depicting the mesenchymal-like (x-axis), myoblast-like (y-axis) and progenitor-like (point colour) meta-program scores. Dotted lines correspond to the cut-offs used to define discrete cell states. c Proportion of cells within each discrete state, per FN tumour. d Representative RNA fluorescence in-situ hybridisation (RNA-FISH) images depicting the expression of mesenchymal-like (MES = TGFBI) and progenitor-like (PROG = FGFR4) cell state marker genes in FN tissue samples. DAPI counterstaining is shown in grey. Scale bars equivalent to 25 µm. e Diffusion maps projection of FN RMS single cells, coloured by pseudotime value, overlaid with the RNA velocity vector field. f Heatmap depicting the Pearson correlations between cell-state scores, and the logistic regression-defined similarity scores (logits) for each normal myogenic cell type. Myogenic differentiation schematic was created with BioRender. Source data are provided as a Source Data file.