Fig. 1

Transcriptional comparison of 50 breast cancer cell lines with 1025 breast cancer tumour samples in The Cancer Genome Atlas suggests overall transcriptional similarity. a, b Scatterplots of mean expression values (log₂[transcripts per million + 1]) of 16,282 coding genes in cell lines (horizontal) and tumours (vertical) for oestrogen receptor–positive (ER+) (a) and oestrogen receptor–negative (ER−) (b) samples reveal that the two datasets are largely comparable with more outliers that are high in tumours and low in cell lines than vice versa. Blue lines indicate linear regression; blue shading indicates 95 % prediction interval for regression. c The 5000 most variable genes were used for principal component analysis, and the first two principal components (PC1 and PC2, respectively) explaining 28 % of the variance are displayed. Cell lines cluster apart from tumours on an axis largely explained by ER status. Colours of the points indicate sample types: ER+ tumour (blue), ER− tumour (red), ER+ cell line (green) and ER− cell line (black). d PC1 of the breast cancer tumours is highly correlated with ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumours using Expression data) paradigm stromal scores (r = 0.74)