Table 3.
Breast Cancer Pathway Analysis Summary
| Met. | Subtypes | # Pathways a | Up in class 1 | Up in 2 | % DE genes |
|---|---|---|---|---|---|
| GR | Basal vs. Lum. A | 324 (362) | 324 (357) | 0 (5) | 33 (61) |
| GS | Basal vs. Lum. A | 26 | 26 | 0 | 33 (61) |
| GR | Lum B. vs. Lum. A | 322 (369) | 322 (369) | 0 (0) | 10 (32) |
| GS | Lum B. vs. Lum. A | 62 | 57 | 5 | 10 (32) |
| GR | Basal vs. Lum. B | 115 (227) | 102 (193) | 13 (34) | 23 (53) |
| GS | Basal vs. Lum. B | 1 | 1 | 0 | 23 (53) |
aFor GRAPE significance threshold is Bonferroni P below 0.01, threshold of nominal 0.01 P-value shown in parentheses. For GSEA significance threshold is FDR q-value below 0.25