Table 3.
Correlations of cancer-adjacent gene expression with biologically relevant signatures, by microenvironment subtype and tumor characteristics
| Microenvironment subtype | Tumor subtype/tumor characteristics | ||||||
|---|---|---|---|---|---|---|---|
| Signature | Number of genesa |
Active N (%) N = 27 |
Inactive N (%) N = 45 |
Claudin low N (%) N = 9 |
Non- Claudin low N (%) N = 63 |
ER positiveb N (%) N = 44 |
ER negative N (%) N = 22 |
| TWIST | 831/794/664 | ||||||
| positive | 25 (92.6) | 7 (15.6) | |||||
| negative | 2 (7.4) | 38 (84.4) | |||||
| P = 5.7e-11 | |||||||
| Claudin Low | 807/754/478 | ||||||
| Positive | 26 (96.3) | 7 (15.6) | 6 (66.7) | 27 (42.9) | |||
| Negative | 1 (3.7) | 38 (84.4) | 3 (33.3) | 36 (57.1) | |||
| P = 3.6e-12 | P = 0.28 | ||||||
| TGFβ | 217/207/181 | ||||||
| Positive | 18 (66.7) | 15 (33.3) | |||||
| Negative | 9 (33.3) | 30 (66.7) | |||||
| P = 7.7e-3 | |||||||
| DTF | 511/451/351 | ||||||
| Positive | 16 (59.3) | 16 (35.6) | |||||
| Negative | 11 (40.7) | 29 (64.4) | |||||
| P = 0.086 | |||||||
| ER Response | 754/700/407 | ||||||
| positive | 14 (51.9) | 21 (46.7) | 25 (56.8) | 5 (22.7) | |||
| negative | 13 (48.1) | 24 (53.3) | 19 (43.2) | 17 (77.3) | |||
| P = 0.80 | P = 0.010 | ||||||
a Correlations are presented using data for genes that mapped and had IQR > than median IQR. The number of genes for each signature are given as total number of genes in published signature/number of genes that mapped to the dataset/number of genes in dataset with IQR > median IQR. This final number of genes was used to perform association analyses.
b six tumors were missing ER status.