Extended Data Figure 4 : Ependymoma enhancer supporting data.

From: Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Extended Data Figure 4

a, Number of unique H3K27ac peaks detected by MACS1.4 (P < 1 × 10−9 cut-off) with increasing sample number in the Heidelberg cohort (n = 24 independent samples). b, Box plot of gene expression values comparing typical enhancer (n = 9,826 genes) versus super enhancer (n = 1,682 genes) associated genes. Statistical analysis was assessed using a two-sided Wilcoxon rank-sum test. Box plots show the centre (median), upper and lower quartile range, and dotted line indicating minima and maxima. c, Frequency of enhancer and super enhancer regions as a function of size in base pairs. d, Dot plots illustrating the numbers of super enhancers detected in the Heidelberg (n = 24 independent samples), Toronto (n = 18 independent samples) and normal brain (n = 7 independent samples) cohorts. The horizontal bar indicates the mean. e, Heatmap illustrating significant gained and lost enhancer loci in both ependymoma cohorts compared to normal brain samples. Comparisons were evaluated using a two-sided Wilcoxon rank-sum test with FDR correction and a cut-off of FDR <0.05. f, Example plots of normalized and scaled H3K27ac RPKM profiles at example ependymoma candidate genes in Heidelberg ependymomas and normal brain (NB) (n = 32 independent samples). g, Comparison of gene expression of ependymoma super-enhancer-associated genes derived from ref. 11 (n = 83 independent samples) with normal brain (n = 172 independent samples). Statistical analysis was assessed using a two-sided Wilcoxon rank-sum test. h, Table comparing the number and per cent confirmation between the Heidelberg (n = 24 independent samples) and Toronto ependymoma cohorts (n = 18 independent samples). i, G-Profiler pathway-enrichment analysis of ependymoma-specific super-enhancer-associated genes in the Toronto cohort (n = 18 independent samples), with statistical significance determined using a hypergeometric test. j, Overlap analysis measured by a two-sided binomial test between tumour-specific ependymoma super enhancers and cancer census genes from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. k, Classification of tumour-specific ependymoma super enhancer genes also found in the COSMIC database29 as tumour suppressor genes (n = 12), oncogenes (n = 26), or unknown (n = 21).