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Enhancer and super-enhancer (SE) calls were obtained using the Rank Ordering of Super-enhancer (ROSE2) algorithm11. We selected SEs assigned to transcription factors (TFs)60,61, and for each sample, we obtained the ranks of all TF SEs. Considering only the top 5% TFs by median ranking in NEPC or PRAD, we applied a one-sided Mann–Whitney U-test to identify lineage-enriched TF SEs (FDR = 10%).
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