Fig. 5

Integrated mutational and transcriptomic analysis reveals clonal selection and degenerate state in cancer evolution. A, B The horizontal bar plots of evolution path analysis (A) and clonal selection analysis (B) with mutated gene expression. “metastasis” versus “primary” (LC: Metastasis panel) and “progression disease (PD),” “partial response (PR),” and “stable disease” (SD) in lung cancer (LC: drug-response panel). “good response” and “poor response” in CML sampled at diagnosis (CML: drug-response panel). Only the top 5 cancer signatures and top 5 metabolisms for “metastasis,” “PD,” and “poor response” with q value <  = 0.1 were shown. The bar indicates the mean Spearman correlation coefficient for each group. The standard error is shown as an error bar. Terms in red are cancer related and black metabolism related. C Fraction of significant features from “metastasis,” “PD,” or “poor response” that was verified by literature search. D The overlap between significant features (q value <  = 0.1) in mutational analysis and transcriptional analysis in the evolutionary path and clonal selection analyses. E The overlap between significant features (q value <  = 0.1) in transcriptional analysis from the “metastasis” or “PD” group and mutated gene expression analysis in the evolutionary path and clonal selection analyses. D, E For the chemotherapy response analysis in lung cancer, we merged PR and SD. We considered the overlap if the feature is enriched in the same group. F Number of significant features of “metastasis,” “PD,” or “poor response” from Figure S6A and B for mutational analysis (upper panel) and Figure S7A and B for transcriptional analysis (lower panel). G Significant features overlap with the same enrichment group (mutational signature, transcriptional signature, and mutated gene expression; q value <  = 0.1) between the evolution path analysis and clonal selection analysis. D, E, G The bar plots indicate the observed overlap/expected overlap (Obs/Exp). Please see the detailed procedure in the “Methods” section