Table 2 |
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|
Comparison of cluster 1 and cell types/subtypes from published gene lists |
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|
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. |
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|
Haakensen et al. BMC Medical Genomics 2011 4:77 doi:10.1186/1755-8794-4-77 |
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