Extended Data Figure 3 : Preprocessing and clustering of ependymoma H3K27ac profiles.

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

Extended Data Figure 3

a, b, Box plots of H3K27ac enhancer profiles (n = 556,676 enhancer loci evaluated per sample) before quantile normalization for both Heidelberg (n = 24 independent samples) (a) and Toronto (n = 18 independent samples) (b) cohorts compared to Roadmap Epigenomics and ENCODE cohorts (n = 98 independent samples). Box plots are shown with the centre (median), upper and lower quartile range, and dotted line indicating minima and maxima per sample. c, d, Box plots of H3K27ac enhancers after quantile normalization for both Heidelberg (n = 24 independent samples) (c) and Toronto (n = 18 independent samples) (d) cohorts compared to the Roadmap Epigenomics cohort (n = 98 independent samples). e, f, Unsupervised hierarchical clustering of enhancer profiles as measured using the top 10,000 variant enhancer loci identified in the Roadmap Epigenomics cohort with the Heidelberg (n = 122 independent samples) (e) and Toronto cohorts (n = 116 samples) (f) and compared in a pair-wise fashion using a Spearman correlation.