Fig. 1: Annotation of alternative promoters in hepatocellular carcinoma (HCC) patients.

a A schematic workflow to describe the mapping of CAGE-seq reads to define consensus transcript clusters (TCs) across the cohort. b Barplot shows the overlap of HCC TCs with the annotated FANTOM5 CAGE peaks and open chromatin peaks from ENCODE and TCGA. c A schematic workflow to annotate intragenic CAGE TCs as high-confidence alternative promoters. The workflow includes multiple filtering steps to exclude TCs that lack promoter features. d Distance between 5′ ends of novel TSSs and 5′ ends of RNA-seq and EST transcripts. e Classification of expressed genes into single promoter (SP) and multi-promoter (MP) genes based on the number of promoters. The promoter with the highest expression level (represented by arrow height) is assigned as the reference promoter. f Venn diagram shows the intersection of novel alternative promoters with known MP genes. g Enrichment of signature genes in MP genes compared to SP genes. P values were computed using a two-tailed Fisher’s exact test. h Distribution of survival-associated genes with SP and MP genes. The MP genes were significantly associated (P = 1.06E−247; Fisher’s exact test) with survival outcome. i The scatter plot shows the association of overall survival for reference and alternative promoters. P values were computed using the chi-squared test.