Fig. 5

13 circRNAs correlate with bladder cancer progression. Heatmap of 13 circRNAs that correlate with bladder cancer progression independently of the linear transcript and the mRNA, together with ciRS-7. Expression levels in counts per million (CPM) are denoted with a color gradient (right part). White denotes no reads. Samples are ordered according to their EORTC score. For each sample, colored bars above expression heatmap denote stage, grade, prognostic class, library size, and EORTC score and whether or not it progresses to muscle-invasive bladder cancer (T2+). Properties of individual circRNAs are denoted with larger colored bars (left of expression heatmap). Properties that can be represented by Yes/No/NA: (iii) Known cancer gene (does the circRNA arise from a known cancer gene); (iv) Circ-to-lin ratio > 1 (is the average circular-to-linear expression level across all samples greater than 1); (v) SCE, obs > exp (is the observed SCE coverage higher than expected SCE coverage based on exon size); (vi) miRNA, obs > exp (is the observed miRNA coverage higher than expected miRNA coverage based on exon size); (vii) ADAR correlation (is circRNA expression correlated with ADAR expression, Spearman correlation); (viii) Quaking correlation (is circRNA expression correlated with Quaking expression, Spearman correlation); (ix) Cell lines (are the circRNAs detected in at least one bladder cancer cell line); (x) EORTC correlation (is circRNA expression correlated with EORTC score, Spearman correlation); (xi) Diff. exp., class 1 versus 2 (differential expression analysis between class 1 and 2, Wilcoxon rank sum test); (xii) circ-to-lin diff. exp., class 1 versus 2 (differential expression analysis of the circular-to-linear ratio between class 1 and 2); (xiii) KM circ (Kaplan–Meier analysis of the circular transcript), (xiv) KM lin (Kaplan–Meier analysis of the corresponding linear transcript); (xv) KM mRNA (Kaplan–Meier analysis of the parent gene (mRNA)). The Benjamini–Hochberg procedure were used for multiple testing correction and FDR < 0.1 were declared significant. Properties that range high/far to low/near: (i) Conservation core splice sites (average conservation of the four core nucleotides involved in splicing); (ii) Alu repeats (the distance between the pair of inverted homologous Alu repeats in closest proximity with the circle); (xvi) No. of tissues (in how many of the 113 tissues is the circRNA expressed). (xvii) Expression levels in CPM in bladder tissue are denoted with the same color gradient as the heatmap