Fig. 4: Gene expression characteristics and relation to chemotherapy response.
a Visualisation of four identified consensus gene expression subtypes by selected gene sets. b Gene expression subtypes compared to chemotherapy response. c Kaplan–Meier survival analysis showing the probability of overall survival for patients with and without Ba/Sq gene expression subtype. d Number of mutations for gene expression subtypes. e Heatmap showing relative expression values for identified regulons and deconvoluted immune cells. f Regulon clusters compared to gene expression subtypes. g Regulon clusters in relation to response to chemotherapy. h Immune score across the identified gene expression subtypes. i Immune score compared to response to chemotherapy. j Summarized expression of the antigen-presenting machinery for immune hot (above median immune score) samples stratified by RECIST 1.1 response values. Only one tumor was classified as NE-like and was therefore omitted from this figure. Missing data is depicted in gray. P-values were calculated using a Fisher’s exact test for categorical variables, a Wilcoxon rank-sum test for continuous variables and a log-rank test for comparing survival curves. For all boxplots, the center line represents the median, box hinges represent first and third quartiles, whiskers represent ±1.5 × interquartile range (IQR) and points represent outliers. Source data are provided as a Source data file.
