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Fig. 5 | Genome Biology

Fig. 5

From: MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Fig. 5

M2A reveals alternate promoter usage in RMS and EWS. a An analysis of alternate primary promoter usage between RMS subtypes ERMS and ARMS shows that M2A appropriately predicts subtype-specific promoter usage in PDZRN3, a known target of the PAX3/7–FOXO1 fusion protein, which is consistent at the observed values of H3K27ac, H3K4me3, RNA-seq, and DNA methylation. Partial M2A input (DNAm 2500 bp windowed average) is shown to emphasize the DNAm patterns in the genomic region surrounding the TSS ± 25 kb. b Alternate promoter usage in EWS patient samples with and without TP53 mutations were incorporated in a Cox proportional hazards model, highlighting the potential prognostic value of the isoforms identified by M2A

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