Figure 4
Molecular-Based Score (MBS) entities are associated with differential transcriptomic programs. (A–C) Gene set enrichment analysis (GSEA) with compiled modules from Hallmarks of the molecular signatures database. * indicates a GSEA for Reactome database. Specific comparisons are indicated in the figure. False discovery rate (FDR) < 0.25, normalized enrichment score (NES) >|1.5|. (D–F) Representative enrichment graphs from ranked GSEA analysis. Specific comparisons are indicated in the figure. (G–I) Volcano plots depicting the extent (x-axis) and significance (y-axis) of differential gene expression for each gene comparing favourable versus (vs) intermediate, favourable vs adverse, and intermediate vs adverse MBS categories, respectively. (J) Heat map summarizing expression of the top 200 differentially expressed genes across MBS entities. Colour intensity represents the by ɀ-score within each row. Expression values for genes represented by multiple probes reflect the median across-array intensity and the gene expression profiles were clustered using the K-means algorithm. Heat map was constructed using Morpheus (https://software.broadinstitute.org/morpheus).
