Fig. 2
From: Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles
The top 1 % differentially expressed genes in the combined expression dataset. a Heatmap representation of the top 1 % of differentially expressed genes (adjusted p value by t test) in cell lines compared with tumours. In all cases, the direction of difference favoured high expression in tumour samples. All genes were investigated in tumours for potential correlation with the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumours using Expression data) paradigm stromal and immune scores. Of the top 163 differentially expressed genes, 134 genes were found to have a Pearson’s correlation coefficient >0.5 (data not shown) with either stromal or immune score. Differential expression (box plot) and stromal correlations (scatterplot) are displayed for representative genes (b, c) POSTN, (d, e) MMP11 and (f, g) HGF. Box plots (b, d, f) 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. Scatterplots (c, e, g) show gene expression values (log2(TPM+1)) versus stromal score (ESTIMATE algorithm) of tumours. Pearson’s correlation coefficient is displayed in the upper left corner