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. 2022 Apr 26;14(9):2172. doi: 10.3390/cancers14092172

Figure 1.

Figure 1

Changes in gene expression in patient-derived scaffold cultures cluster in cell line-dependent manner. Unsupervised analyses were applied to the expression of 14 genes associated with relevant cancer processes in 84 patient-derived scaffolds (PDSs) cultured with three different cell lines. (A) Principal component analysis (PCA) scores showing the PDSs cultured with MCF7 (blue), T-47D (green), and MDA-MB-231 (red). (B) PCA loading plot illustrating the genes’ contribution to the separation in the plot (A). Colour code markers: green, proliferation; blue, pluripotency; red, breast cancer stem cells (CSC); and purple, epithelial-mesenchymal transition (EMT). (C) Heatmap visualization grouping the genes (columns) and PDSs (rows) using average linkage as clustering method and Euclidean distances as the distance measure. Gene expression in PDSs is expressed in log2-scale, and relative to 2D controls for each cell line.