Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference
Fig 7
Detection of functional impact of SGA-FIs reveals functional connections among SGA-FIs.
A. Top 45 SGAs-FIs (regulating the largest number of DEGs) and their relationships with 17 cancer hallmark gene sets. The value in a cell represents the fraction of genes in a hallmark gene set that is covered by the target DEGs of each SGA-FI. B-E. Top 15 SGA-FIs that share the most significant overlapping target DEGswith PIK3CA, TTN, CSMD3, and ZFHX4. An edge between a pair of SGA-FI indicate that they share significantly overlapping target DEG sets, and the thickness of the line is proportional to negative log of the p-values of overlapping target DEG sets. F. An “oncoprint” illustrating the causal relationships between the DEG RUNDC3B and its 3 main drivers according to TCI, namely, PIK3CA, CDKN2A, and PTEN. Each column corresponds to a tumor; green bars indicate tumors in which TCI designated each of the three SGA genes as a driver, regardless of what DEGs it was driving in a given tumor. The causal relationship is color-coded, which illustrates which SGA-FI is predicted by TCI to cause the RUNDC3B DEG event; the blue bar indicates the DEG events that were assigned to SGA-FIs other than the above 3 SGA-FIs; gray bars indicate a wild type genomic and transcriptomic status.