Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference
Fig 4
SM and SCNA perturbing a gene exert common functional impact.
A. Combining SM and SCNA data drisrupts the correlation structure among genes enclosed in common SCNA fragments. The chromosome cytobands enclosing three example genes (PIK3CA, CSMD3, and ZFHX4) are shown. The bar charts show the frequency of SCNA (red, standing for amplificaton) and SM (green). The disequilibrium plots beneath the bar charts depict the correlationship among genes within a cytoband. B-E. The SGA patterns, i.e. SM and CN amplification/deletion, across different cancer types for PIK3CA, CDKN2A, CSMD3 and ZFHX4, F-I. SGA-FI target DEG call rates in SM tumors and CN amplification/deletion for PIK3CA, CDKN2A, CSMD3 and ZFHX4. J-M. Venn diagrams illustring the relationships of DEGs caused by CN amplication/deletion and SM for PIK3CA, CDKN2A, CSMD3 and ZFHX4.