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.

Haakensen et al. BMC Medical Genomics 2011 4:77   doi:10.1186/1755-8794-4-77

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