To prioritize the gene sets important for tumor progression, we scored the above 38 gene sets across tumor clusters (Fig. 4f) and identified seven gene sets that are significantly associated with higher tumor stage (FDR < 0.1), namely inflammatory response (Fig. 4g), unfolded protein response, TGF-β signaling, TNF-α signaling via NF-κB, IL2-STAT5 signaling, IL6-JAK-STAT3 signaling, and apical junction. This evidence concerns the gene TNF and neoplasm.