1. Derivation and application of cancer‐specific epithelial‐mesenchymal transition (EMT) signature A six‐step scheme illustrating the generation of a cancer‐specific EMT signature.
Derivation and application of cancer‐specific epithelial‐mesenchymal transition (EMT) signature A six‐step scheme illustrating the generation of a cancer‐specific EMT signature. Note that tumours and cell lines have their own cancer‐specific EMT signatures. (Top right panel) Red and green bars on sample enrichment score (ES) bar chart indicate, respectively, mesenchymal‐like (Mes) and epithelial‐like (Epi) samples selected for building the BinReg EMT signature. (Middle right panel) Heatmap of the EMT signature from Significance Analysis of Microarray (SAM)/Receiver Operating Characteristics (ROC) analysis. The colour bar shows the EMT phenotype probability of cell line or tumour samples, sorted from most Epi to most Mes. Red and green bars indicate Mes and Epi samples selected for SAM/ROC analysis. (Bottom right panel) Plots of empirical cumulative distribution function of Mes (red) and Epi (green) gene sets. Dot plot of EMT score (mean ± SEM) for breast cancer cell lines (n = 34) with spindle‐ and non‐spindle‐like morphologies. Mann–Whitney U‐test P‐value is shown. Immunohistochemistry staining heatmap of Oestrogen Receptor (ER), Progesterone Receptor (PR), and Epi (CDH1, ERBB2, CK19) as well as Mes (CK5, VIM, CDH2) markers (black = low, red = high, white = no data). Breast cancer cell lines (n = 39) are aligned from the most Epi to most Mes based on the EMT score, as shown by the bar chart. Dot plot is the ‐log10P‐value of two‐sample Kolmogorov–Smirnov test. Arbitrary threshold of P < 0.001 was used to define Epi, intermediate and Mes cell lines. Breast cancer cell line microarrays and subtype are from GSE16795 (Hollestelle et al, 2010). Subtype colour code: blue, Luminal; maroon, Basal.
Tuan Zea Tan et al. EMBO Mol Med. 2014;6:
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