Fig. 3: Gene set enrichment by GSEA for pairs of BCCS subtypes.

Enrichment for each Hallmark v7 gene set was tested between each pair of PCS1–4 and NCS1–3 and all three study cohorts using GSEA. A gene set was considered enriched between a pair of subtypes if the adjusted p-value was < 0.05 in all three cohorts. A GSEA test for enrichment in A versus (v) B reported the normalized enrichment score (NES); NES was positive if expression was enriched in A compared to B, and NES was negative if expression was enriched in B compared to A. A Hallmark gene set is omitted if it was not significantly enriched in any test. A tile is colored green (respectively, goldenrod) for the given pair and gene set, if in all three study cohorts, the adjusted p-value was < 0.05 and NES was positive (respectively, negative); a tile is gray if the adjusted p-value was ≥ 0.05 in some cohort.