Figure 4

Prognostic significance of copy number alteration (CNA) in functionally unknown prognostic genes identified by IPP. (A) Among all prognostic genes (n = 557) for luminal breast cancer, 29.1% and 4.8% of the adverse and favorable prognostic genes, respectively, were not assigned to any functional group by Reactome pathway enrichment analysis (upper panel). Kaplan-Meier curves show the difference in disease-free survival (DFS; days) according to the CNA states (amplification, neutral, or deletion) of CADPS2 and METTL17, favorable and adverse prognostic genes, respectively, which were not assigned to any functional group by Reactome pathway enrichment analysis (lower panel). (B) Among all prognostic genes (n = 557) for triple-negative breast cancer, 21.0% and 10.4% of adverse and favorable prognostic genes, respectively, were not assigned to any functional group by Reactome pathway enrichment analysis (upper panel). Kaplan-Meier curves show the differences in overall survival (OS; days) according to the CNA state (amplification, neutral, or deletion) of PARP8 and TULP2, favorable and adverse prognostic genes, respectively, which were not assigned to any functional group by Reactome pathway enrichment analysis (lower panel). The colors of the Kaplan-Meier curves indicate the CNA states (purple: amplification, black: neutral, green: deletion). Each n on the Kaplan-Meier curves indicates the number of patients included in that CNA state.