Fig. 4
From: Towards resolution of the intron retention paradox in breast cancer
Breast cancer-specific gene expression and RBP analysis. A Volcano plots showing differentially expressed genes in nine tumour types vs adjacent healthy tissue. The dashed lines represent the p value cut-off (horizontal; p < 0.05) and fold change threshold (vertical |FC| ≥ 1). See Fig. 1A for cancer-type abbreviations. Highlighted in blue are genes that are exclusively differentially expressed in BrCa, while those in red represent RBPs within this subset. B Heatmap of genes specifically differently expressed in BrCa (represented by colour-coded z-score). Annotation bar (left) shows the colour-coded correlation coefficient between gene expression and number of IR events in each sample. C Bar plots show the frequencies with which known binding motifs occur around the splice sites (50 nt up-/downstream) of differentially retained (IR; dark blue) and non-differentially retained introns (NR; light blue). Differences in average frequencies were determined using Student’s t test. *p < 0.05, ***p < 0.001, ****p < 0.0001, NS—not significant