Fig. 1: lncRNA expression in breast cancer subtypes.
From: Subtype and cell type specific expression of lncRNAs provide insight into breast cancer
Hierarchical clustering of log2(TPM + 1) of 4108 lncRNAs expressed above filtering thresholds (see Methods) in the SCAN-B (a), and TCGA-BRCA (b) cohorts. Estrogen Receptor (ER) and Her2 status, as well as PAM50 subtypes are annotated at the top of the heatmap. The expression gradient (blue to red) represents scaled and centered log2(TPM + 1). c–e Dot plot of the log Fold Change (FC) from the differential expression analysis using a fitted Limma model (lmfit) and moderated t-statistic (eBayes) between patients of different subtypes in SCAN-B (x-axis) and TCGA-BRCA (y-axis). Each dot represents a lncRNA, while the colour indicates the subtype with the highest expression c ER positive (blue) and ER negative (red), d Her2 negative (dark blue) and Her2 positive (pink). e Luminal A (dark blue), and Luminal B (light blue). Gray dots are lncRNAs that are not significantly differentially expressed, while black dots represent lncRNAs with opposite fold change (FC) in the two cohorts. The number of patients in each clinical group were as follows: ER positive (n = 2409 and n = 807), ER negative (n = 504 and n = 237), Her2 positive (n = 458 and n = 114), Her2 negative (n = 2845 and n = 650), Luminal A (n = 1769 and n = 562), and Luminal B (n = 766 and n = 209) in SCAN-B and TCGA-BRCA respectively.
