Table 2. Up-regulated BH3-only candidate genes in breast cancer subtypes.
The logFC is indicated in the table, all the results refer to an FDR < 0.05. Empty lines indicate that the gene is not differentially expressed in the corresponding comparison. We do not report the comparison between LumA and LumB since it results in only three BH3-only genes with signs of deregulation (see S4 Table). We show only BH3-containing genes for which we find differential expression in at least two comparisons, for sake of clarity. The full list is reported in S4 Table.
| GENE | Bcl-2 interactor | Cancer vs Normal | Basal vs HER2 | Basal vs LumA |
Basal vs LumB |
Basal vs Normal |
HER2 vs LumA | HER2 vs LumB |
HER2 vs Normal |
LumA vs Normal |
LumB vs Normal |
|---|---|---|---|---|---|---|---|---|---|---|---|
| RTN1 | Bcl2l1 | -1.65 | -1.13 | -2.12 | -1.44 | -1.91 | |||||
| NMT2 | Bcl-2 | -1.57 | 1.14 | 1.06 | 1.38 | -1.82 | -1.74 | -2.06 | |||
| CLU | Bax, Bcl2l1 | -1.30 | -1.15 | -1.02 | -2.17 | -1.47 | -1.01 | -1.15 | |||
| ZNF219 | Bcl2l1 | -1.16 | -1.55 | -1.47 | -1.21 | ||||||
| ECM1 | Mcl-1 | 1.22 | -1.72 | -1.86 | -1.85 | 1.44 | 1.58 | 1.58 | |||
| SLC9A3R1 | Bcl2a1 | 1.08 | -1.42 | -1.48 | -2.17 | 1.22 | 1.28 | 1.97 | |||
| HRK | Bcl-2, Bcl2l1, Bcl2l2, Mcl1, Bcl2a1, Bax | -1.34 | 2.22 | 3.79 | 3.38 | -1.33 | 1.57 | 1.16 | -2.45 | -2.04 | |
| IRS2 | Bcl-2, Bcl2l1 | -1.88 | 1.05 | -1.92 | -1.27 | -1.07 | -2.98 | -1.71 | -1.91 | ||
| NLRP1 | Bcl-2, Bcl2l1 | -1.35 | -1.27 | -1.43 | -1.28 | -1.65 | |||||
| LGALS3 | Bcl-2 | -1.04 | -1.19 | -1.46 | |||||||
| RRAS | Bcl-2 | -1.10 | -1.17 | -1.01 | -1.39 | ||||||
| ITPR1 | Bcl-2 | -1.33 | -1.46 | -2.12 | -1.74 | -2.92 | -1.45 | -1.17 | |||
| CFLAR | Bcl2l1, Bax | -1.00 | -1.04 | -1.27 | |||||||
| NR4A1 | Bcl-2, Bcl2l10, Bcl2a1 | -2.63 | -2.64 | -2.72 | -2.55 | -2.83 | |||||
| STARD9 | Mcl-1 | -2.21 | -2.10 | -2.50 | -2.16 | -2.43 |