Table 1. Cross tabulation of intNMF subtypes with TCGA subtypes and iCluster subtypes using multiplatform Breast cancer data.
The summary table, followed by cross tabulation tables, represents the receptor status for estrogen (ER), progesterone (PR) and human epidermal growth factor 2 (HER2) presented as percentage of their presence in each of the six intNMF clusters; and somatic mutations in four genes TP53, PIK3CA, GATA3 and MAP3K1.
| TCGA Subtypes | intNMF | Total | ||||||
|---|---|---|---|---|---|---|---|---|
| C1 | C2 | C3 | C4 | C5 | C6 | |||
| Cluster of Clusters | (1) HER2 | 2 | 4 | 25 | 4 | 1 | 3 | 39 |
| (2) Basal | 0 | 2 | 1 | 66 | 0 | 3 | 72 | |
| (3) Luminal A | 25 | 23 | 6 | 3 | 12 | 92 | 161 | |
| (4) Luminal B | 17 | 24 | 8 | 1 | 10 | 16 | 76 | |
| Total | 44 | 53 | 40 | 74 | 23 | 114 | 348 | |
| iCluster | C1 | 11 | 14 | 11 | 4 | 5 | 71 | 116 |
| C2 | 0 | 0 | 9 | 68 | 0 | 0 | 77 | |
| C3 | 33 | 39 | 20 | 2 | 18 | 43 | 155 | |
| Total | 44 | 53 | 40 | 74 | 23 | 114 | 348 | |
| ER+ (%) | 95.5 | 94.3 | 60.0 | 13.5 | 95.7 | 97.4 | ||
| PR+ (%) | 86.4 | 71.7 | 42.5 | 5.4 | 82.6 | 86.8 | ||
| HER2+ (%) | 4.5 | 9.4 | 95.0 | 1.4 | 4.3 | 6.1 | ||
| TP53 (%) | 31.8 | 32.1 | 57.5 | 85.1 | 26.1 | 13.2 | ||
| PIK3CA (%) | 29.5 | 33.9 | 27.5 | 8.1 | 21.7 | 55.3 | ||
| GATA3 (%) | 6.8 | 16.9 | 10.0 | 1.4 | 8.7 | 17.5 | ||
| MAP3K1 (%) | 29.5 | 5.7 | 0.0 | 0.0 | 13.0 | 15.8 | ||