Fig. 4
From: Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles
The top 1 % of differentially expressed genes after filtering out genes correlated with stromal and immune scores in tumours. a The list of differentially expressed genes was refined for correlation with stromal and immune signatures, uncovering novel differentially expressed genes more likely to genuinely reflect changes induced by cell culture. Heatmap representation of the filtered top 1 % of differentially expressed genes (|r| < 0.2; adjusted p value by t test) in cell lines compared with tumours. Differential expression (box plot) and stromal correlations (scatterplot) are displayed for representative genes: (b, c) KRT17, (d, e) NDUFB4 and (f, g) AHRR. b, d, f Boxplots show gene expression values (log2([transcripts per million {TPM}+1]) stratified by sample source (cell line or tumour). Boxes represent interquartile ranges, and points represent individual sample values. c, e, g Scatterplots show gene expression values (log2[TPM+1]) versus stromal scores (ESTIMATE algorithm [Estimation of STromal and Immune cells in MAlignant Tumours using Expression data]) of tumours. Pearson’s correlation coefficient is displayed in the upper left corner