Table 2.
Comparison of cluster 1 and cell types/subtypes from published gene lists
| Comparison | Reference | Cluster 1 resembles | P-value |
|---|---|---|---|
| Epithelial vs stem-like cell | Shipitsin, 2007 | Stem-like cell | 2.20E-16 |
| Stroma vs epithelium | Finak, 2006 | Stroma | 2.20E-16 |
| Mesenchymal vs epithelial | Jechlinger, 2003 | Mesenchymal | 6.90E-14 |
| Revised subtypes | Herschkowitz, 2007 | Claudin-low | 1.52E-12 |
| Fibroblasts vs epithelial cells | Casey, 2008 | Fibroblasts | 1.9E-12 |
| Risk predictor | Chen, 2009 | Low risk | 1.30E-09 |
| Stem-like cell vs epithelial | Liu, 2007 | Stem-like | 1.30E-05 |
| Myoepithelial vs progenitor | Raouf, 2008 | Progenitor | 2.40E-05 |
| Luminal vs progenitor | Raouf, 2008 | Progenitor | 0.001 |
| Stem-like vs progenitor cells | Villadsen, 2007 | Lineage restricted progenitor | 0.008 |
| Myoepithelial vs luminal | Jones, 2004 | (Myepithelial) | 0.06 |
| Classical subtypes | Sorlie, 2001 | - | 0.76 |
*) Chi squared test for significance
Chi-squared test is used to illustrate the extent to which genes describing different cell types are equally regulated in the two clusters. Significant p-values are in bold type. For more information on the publications and comparisons, see Supplemental file 3, Table S3.