Table 1.
Therapeutic compounds that show significant subtype specificity
| Compound | Target | Basal vs. claudin-low vs. luminal | Basal and claudin-low vs. luminal | ERBB2AMP vs. not ERBB2AMP | Subtype specificity |
| Lapatinib | EGFR, ERBB2 | 7.23E-02 | 3.34E-02 | 2.26E-06 | Luminal/ERBB2AMP |
| Sigma AKT1-2 inh. | AKT1, AKT2 | 1.17E-03 | 2.63E-04 | 1.29E-01 | Luminal |
| GSK2126458 | PIK3C A/B/D/G | 1.27E-03 | 1.27E-03 | 8.67E-02 | Luminal/ERBB2AMP |
| Gefitinib | EGFR | 4.89E-01 | 3.35E-01 | 4.14E-03 | ERBB2AMP |
| BIBW 2992 | EGFR, ERBB2 | 6.93E-01 | 8.08E-01 | 6.39E-03 | ERBB2AMP |
| GSK2119563 | PIK3CA | 2.85E-02 | 8.11E-03 | 8.67E-02 | Luminal/ERBB2AMP |
| Rapamycin | MTOR | 1.45E-02 | 8.11E-03 | 3.84E-01 | Luminal |
| AG1478 | EGFR | 9.34E-01 | 9.34E-01 | 2.60E-02 | ERBB2AMP |
| Etoposide | TOP2A | 3.34E-02 | 5.13E-02 | 8.89E-01 | Claudin-low |
| LBH589 | HDAC | 5.14E-02 | 3.34E-02 | 3.22E-01 | Luminal |
| Vorinostat | HDAC | 7.23E-02 | 3.34E-02 | 6.89E-01 | Luminal |
| Cisplatin | DNA cross-linker | 8.45E-02 | 4.31E-02 | 8.52E-01 | Basal/Claudin-low |
| Fascaplysin | CDK4 | 4.83E-02 | 4.31E-02 | 3.70E-01 | Luminal |
| Docetaxel | TUBB1, BCL2 | 8.67E-02 | 4.83E-02 | 8.44E-01 | Basal/Claudin-low |
| GSK1070916 | AURK B/C | 5.13E-02 | 4.83E-02 | 4.82E-01 | Claudin-low |
| PD173074 | FGFR3 | 5.13E-02 | 3.68E-01 | 5.06E-01 | Claudin-low |
| Trichostatin A | HDAC | 1.22E-01 | 5.13E-02 | 7.10E-01 | Luminal |
| Triciribine | AKT, ZNF217 | 8.67E-02 | 5.91E-02 | 3.56E-01 | Luminal |
| CGC-11047 | Polyamine analog | 6.51E-02 | 1.25E-01 | 8.08E-01 | Basal |
| Temsirolimus | MTOR | 1.64E-01 | 7.25E-02 | 1.29E-01 | Luminal |
| VX-680 | AURK A/B/C | 2.95E-01 | 4.02E-01 | 7.77E-02 | not ERBB2AMP |
| 17-AAG | HSP90AA1 | 1.83E-01 | 1.10E-01 | 8.67E-02 | ERBB2AMP |
| Erlotinib | EGFR | 9.48E-02 | 2.83E-01 | 2.33E-01 | Basal |
Each column represents q-values for one ANOVA. Compounds are ranked by the minimum q-value achieved across the three tests. BCL2, B-cell CLL/lymphoma 2; CDK4, cyclin-dependent kinase 4; HDAC, histone deacetylase; MTOR, mechanistic target of rapamycin; TOP2A, topoisomerase (DNA) II alpha 170kDa; TUBB1, tubulin β1; ZNF217, zinc finger protein 217.