Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference
Fig 3
The landscape of SGAs and SGA-FIs.
A & B. The distributions of SGAs per tumor and SGA-FIs per tumor of different cancer types. Beneath the bar box plots, the distributions of different types of SGAs (SM, copy number amplification, and deletion) are shown. C. Distribution of SGA-FIs against the alteration frequency and protein length. Pink dots indicate SGA-FIs, and green dots represent SGAs that were not designated as SGA-FIs. A few commonly altered genes are indicated by their gene names, where genes labeled with blue font are well-known drivers, and those labeled with orange font are novel candidate driver. D. Tumor-specific Bayesian prior distributions for top 15 most frequent SGAs. The number above each box represents number of tumors that the corresponding SGA appears in. E. A Circos plot shows SGA events and SGA-FI calls along the chromosomes. Different types of SGA events (SM, copy number amplification, deletion) are shown in tracks 2, 3, and 4, respectively. Track 1 shows the number of times that an SGA is labeled by TCI as an SGA-FI. The gene names denote the top 62 SGA-FIs (some are SGA units) that were called in over 300 tumors with a call rate > 0.8. Genes labeled with blue font are known drivers from two TCGA reports, and orange ones are novel candidate drivers. F. SGA-FIs that were called in less than 300 tumors and with a call rate > 0.9 are shown in this frequency-vs-call rate plot. As before, genes labeled with blue font are known drivers from TCGA studies, and orange ones are novel candidate drivers.