Extended Data Fig. 3: Alternative promoter usage occurs in cancer related genes. | Nature Cell Biology

Extended Data Fig. 3: Alternative promoter usage occurs in cancer related genes.

From: Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression

Extended Data Fig. 3

a) Density plot of the Spearman’s correlation rho values between absolute promoter activity and corresponding gene expression for upregulated APs, downregulated APs and non-differential promoters in genes with differential APs in localized PCa vs benign prostate. b) Pathway enrichment analysis of genes with upregulated APs in mCRPC vs benign. Highlighted in red are pathways enriched for the genes with upregulated APs but not in upregulated genes. P values were calculated using hypergeometric tests. X axis shows the p values without multi-test adjustments, but the coloring was based on Benjamini Hochberg (BH)-adjusted p values. Dashed line shows unadjusted p value 0.05. c) Pathway enrichment analysis result of genes upregulated in mCRPC vs benign prostate. P values were calculated using hypergeometric tests. X axis shows the p values without multi-test adjustments, but the coloring was based on BH-adjusted p values. Dashed line shows unadjusted p value 0.05.

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