Additional file 1:

Supplementary Table 1 includes a complete list of all probe sets that comprise each of the 852 gene sets.

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Additional file 2:

Supplementary Figure 1 presents the same plots as Figure 1 for ER-negative cancers but also includes heat maps of the proliferation set (FDR q = 0.1, p = 0.05) (Supplementary Figure 1A); the genomic grade index set (FDR q = 0.04, p = 0.08) (Supplementary Figure 1B); and the E2F3 pathway gene set (FDR q = 0.2, p = 0.07) (Supplementary Figure 1C). All of these were enriched in the group with pathologic complete response, while no gene set was enriched in the group with residual cancer.

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Additional file 3:

Supplementary Figure 2 presents the same plots as Figure 3 for ER-positive cancers but also includes heat maps of the proliferation set (FDR q = 0.001, p = 0.002) (Supplementary Figure 2A) and the genomic grade index set (FDR q = 0.015, p = 0.01) (Supplementary Figure 2B). In the group with residual cancer, 2 other gene sets showed enrichment including the ER-associated gene list (FDR q = 0.03, p = 0.04) Supplementary Figure 2C) and the mutant p53 gene signature (FDR q = 0.0019, p = 0.07) (Supplementary Figure 2D).

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Additional file 4:

Supplementary Table 2 includes the complete list of probes and genes included in the five enriched gene sets.

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