Fig. 5.

Pathway instability analysis. a Heatmap representation of the 218 GC pathways identified with the Reactome enrichment analysis. Pathways are sorted in columns and grouped according to their corresponding Top Level pathways, with hierarchical clustering applied within the groupings. TMB and MSI class, as well as relapse status and Kodama classification are annotated on the left side for all patients. b, c PI score distribution across  b Kodama classification subtypes and c relapse status, shown for pathways grouped according to selected top level pathways. Each data point indicates a PI score value for an individual GC-related pathway, for each patient separately. Violin plots with horizontal black lines marking the median values convey the overall distribution of PI scores between different patient groupings. Note that since no information on Kodama classification was available for EGC-TCGA patients, these patients are excluded from comparisons between Pen A and Pen B groups. d, e Two-dimensional t-SNE representation of PI scores obtained from 218 pathways of interest, for the combined case series of EGC and TCGA EGC. Clustering overlaid with patients’ d Kodama classification and e TMB classification