| Â | Wnt signaling | Notch signaling |
|---|
| Â | NES | Pvalue | FDR | FWER | NES | Pvalue | FDR | FWER |
|---|
Myoepithelial | -1.47 | 0.03 | 0.06 | 0.04 | 1.08 | 0.35 | 0.34 | 0.74 |
Basal stem/progenitor
|
-1.70
|
< 0.01
|
< 0.01
|
< 0.01
|
1.64
|
< 0.01
|
0.02
|
0.01
|
Luminal Sca1- | -1.08 | 0.33 | 0.64 | 0.37 | 1.08 | 0.32 | 0.62 | 0.45 |
Luminal Sca1+ | -0.68 | 0.99 | 0.99 | 0.74 | 0.83 | 0.77 | 1.00 | 0.93 |
- Gene-set enrichment analysis (GSEA) for Wnt and Notch signaling, as defined by the expression of Wnt or Notch target genes (see Methods) showed a decrease in the Wnt/Notch signaling ratio (strongly negative/positive normalized enrichment scores (NES)), which was specific for the basal stem/progenitor cells. Significance was determined by a cut-off of a nominal P value < 0.01, a false-discovery rate (FDR) < 0.05, and a family-wise error rate (FWER) < 0.05, as suggested by the GSEA homepage [28]. The gene set for Wnt signaling consisted of the reported Wnt targets in mammalian systems (derived from the Stanford Wnt homepage) and is depicted in Additional file 3. The gene set for Notch signaling was derived from the Broad Institute v3.0 and is termed Nguyen Notch1 targets. The number of permutations was set to 1,000, and the permutation type was set to "gene set," because fewer than seven samples existed per phenotype [28]. Otherwise, the default settings were used.
