Fig. 6
Clinical outcome associated with alternative promoter usage. a Scatterplot of adjusted p values for genes with known and novel promoters. Examples of prognostic gene (in blue), prognostic known promoter (in green), and prognostic novel promoters (in red) include TFPI, KRT7, and KDM4A, respectively. b Beeswarm plot showing the average correlation between known and novel promoters. There are more prognostic promoters (known or novel) than prognostic genes and prognostic promoters have lower correlation than prognostic genes, suggesting distinct promoters are independently regulated. c Survival plots showing significant association of novel and known promoters of KDM4A, TFPI, and KRT7 with progression-free survival. d Percentages of known and novel promoters that are differentially expressed in prognostic genes, prognostic promoters, and non-prognostic genes. Deregulated expression of genes and isoforms are prognostic of survival. e Boxplots of the shared and private CD percentage in prognostic genes, prognostic promoters, and non-prognostic genes. Prognostic promoters are enriched with promoter-specific CD regions. f Gene structure of the known and novel ARID1A promoters at the transcript and protein level. Survival curve shows the association between the known and novel promoters of ARID1A with progression-free survival in gastric cancer