Fig. 3

GSVA analysis showed pathway-level/gene set activity differences between the early recurrent and nonrecurrent groups. In the figure, Column 1—Nonrecurrent paired pre-NAC vs. post-NAC), Column 2 – Early recurrent paired pre-NAC vs. post-NAC, and Column 3- post-NAC (early recurrence vs. nonrecurrent). Unsupervised clustering showed two clusters with a distinctive pattern between the two groups (heatmap panel). Cluster 1 gene sets that were upregulated in the early recurrent group included metastasis-promoting gene sets, DNA mismatch repair, and tp53 gene sets. The most commonly observed gene among these gene sets was TUBB4A. Cluster 2 included signaling gene sets such as FOXO, TGFβ, and apoptotic known to be associated with tumor suppression. Details of gene set names and cluster assignments can be found in Additional file 2: Table s8a