Table 3.
Predicted upstream regulators of gene expression differences in breast epithelial organoids isolated from BRCA mutation carriers with BMI≥ 25 relative to carriers with BMI < 25 and associated gene expression in whole breast tissue.
| Organoid upstream regulator | Predicted activation state | Activation z score | P value of overlap | Breast tissue RNA-seq (log2 fold change) | P value |
|---|---|---|---|---|---|
| β-Estradiol | Activated | 4.728 | 2.2 × 10−10 | See Fig. 2C | |
| IL-2 | Activated | 3.402 | 3.1 × 10−2 | 0.563 | 2.3 × 10−1 |
| GDF2 | Activated | 3.217 | 4.9 × 10−3 | −0.081 | 9.8 × 10−1 |
| IL-15 | Activated | 3.152 | 1.5 × 10−3 | 0.299 | 4.1 × 10−5 |
| TNF-SF11 | Activated | 3.125 | 3.2 × 10−2 | −0.757 | 9.7 × 10−2 |
| Insulin | Activated | 3.113 | 6.1 × 10−3 | ||
| IL-4 | Activated | 3.016 | 1.9 × 10−3 | −0.25 | 7.4 × 10−1 |
| TGF-B1 | Activated | 2.942 | 6.0 × 10−9 | 0.455 | 2.2 × 10−8 |
| Hydrogen peroxide | Activated | 2.839 | 3.1 × 10−3 | ||
| IL-3 | Activated | 2.674 | 7.6 × 10−4 | −0.122 | 9.7 × 10−1 |
| CSF1 | Activated | 2.602 | 8.9 × 10−3 | 0.35 | 1.4 × 10−6 |
| Lh | Activated | 2.598 | 1.7 × 10−3 | ||
| Dinoprost (PGF2α) | Activated | 2.569 | 2.9 × 10−2 | ||
| IL-5 | Activated | 2.496 | 5.5 × 10−3 | 0.173 | 6.9 × 10−1 |
| ATP | Activated | 2.443 | 8.7 × 10−3 | ||
| MDK | Activated | 2.433 | 2.9 × 10−2 | −0.34 | 4.4 × 10−3 |
| AGT | Activated | 2.345 | 4.2 × 10−3 | −0.56 | 9.6 × 10−4 |
| ANGPT2 | Activated | 2.329 | 1.1 × 10−3 | 0.38 | 9.2 × 10−5 |
| WNT5A | Activated | 2.292 | 1.7 × 10−3 | 0.184 | 1.3 × 10−1 |
| Pyruvic acid | Activated | 2.156 | 1.5 × 10−3 |