Table 2

Comparison of clinical and molecular characteristics of identified CRC subtypes
iNMF step 1
Molecular feature Type 1 Type 2
No. of tumor samples (AZTS) 28 34
No. of tumor samples (all datasets) 944 762
EMT expression signature mesenchymal epithelial
Survival prognosis poor good
Microsatellite status similar number of MSI and MSS CRC enriched with MSS CRC
iNMF step 2
Molecular feature Subtype 1.1 Subtype 1.2 Subtype 1.3 Subtype 2.1 Subtype 2.2
No. of tumor samples (AZTS) 12 9 7 14 20
No. of tumor samples (all datasets) 313 303 328 313 449
Average percent tumor foci area 79.2 81.4 77.9 82.1 79.7
Average percent tumor cells in foci 76.3 74.5 80.0 73,8 73.7
Average percent stromal cells in foci 18.3 18.3 12.2 21.2 21.2
Average percent inflammatory cells in foci 3.8 7.2 6.4 3.5 4.7
EMT expression signature strongly mesenchymal mesenchymal mesenchymal epithelial epithelial
Tumor location colon/left/rectum/right 0/26/16/15 1/12/1/29 0/12/2/11 1/22/9/37 1/50/11/33
Microsatellite status MSI/MSS 14/15 42/9 2/35 27/31 4/50
Tumor stage enriched in late stage CRC
Gender enrichment Female/Male/Unknown 87/99/0 89/57/0 90/124/1 58/34/0 108/113/0
Up-regulated genes Ca-signaling and SRF-targeted immune system-related transporters stress response and immune system-related cell cycle and amino acid synthesis; genes on 13q13, 13q14, 13q32-34 and 20q11and 20q13

Differences in these characteristics were assessed using all datasets with available annotation.

Schlicker et al.

Schlicker et al. BMC Medical Genomics 2012 5:66   doi:10.1186/1755-8794-5-66

Open Data