Fig. 4

The basal B-specific splicing signature is associated to EMT features. a Heatmap of the Percentage Spliced-In (PSI) values of the 25 cassette exons most informative to classify TCGA basal-like patients into basal B-like (red) or basal A-like (blue). Claudin low tumours are highlighted in green. b, c Sashimi plots displaying ENAH and PLOD2 splicing patterns in randomly selected patients classified as basal A-like and basal B-like. d Changes in alternative splicing of these 25 basal B-specific splicing events is sufficient to properly cluster 55 basal breast cancer cell lines from 3 unrelated sequencing projects into basal B and basal A using t-SNE. Of note, three basal B cell lines, HCC38, MDA-MB-157 and SUM102 were misclassified as Basal A cell lines (red dots). Although HCC38 has also been classified as Basal A in the DepMap portal (www.depmap.org). e Heatmap of the PSI values of the 25 basal B-specific splicing signature in public RNA-seq datasets from four different EMT projects. Basal B-like events have the same splicing patterns as EMT-induced cells