Table 1 Description of the 31 genes that more strongly differentiate ESR1-based BRCA1 subclasses using a fold-change threshold higher or lower than 2 or −2, respectively, and a FDR lower than 5%
Gene name (HUGO) | Description | Chromosome | Start (bp) | End (bp) | Strand | Fold change | FDR P -value |
|---|---|---|---|---|---|---|---|
C10orf116 | Chromosome 10 open reading frame 116 | 10 | 88718168 | 88720646 | + | 3.77 | 6.4207E-04 |
CD133 | Prominin 1 | 4 | 15578950 | 15694453 | − | −2.70 | 1.5661E-02 |
CRABP2 | Cellular retinoic acid binding protein 2 | 1 | 154936034 | 154942232 | − | 2.12 | 7.7835E-03 |
ERBB3 | V-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 12 | 54760159 | 54783395 | + | 2.13 | 1.0152E-05 |
ESR1 | Estrogen receptor 1 | 6 | 152168512 | 152466099 | + | 4.25 | 4.4951E-04 |
F2RL2 | Coagulation factor II (thrombin) receptor-like 2 | 5 | 75947064 | 75954996 | − | 2.12 | 8.3191E-03 |
GATA3 | GATA binding protein 3 | 10 | 8136673 | 8157170 | + | 3.30 | 1.3560E-03 |
GPR98 | G protein-coupled receptor 98 | 5 | 89945799 | 90495789 | + | 3.40 | 6.0975E-03 |
HIST1H1C | Histone cluster 1, H1c | 6 | 26163894 | 26164678 | − | 2.49 | 1.6326E-03 |
HSPB8 | Heat shock 22 kDa protein 8 | 12 | 118100978 | 118116933 | + | 2.86 | 4.4951E-04 |
LAMP3 | Lysosomal-associated membrane protein 3 | 3 | 184322698 | 184363317 | − | −2.29 | 9.6204E-03 |
LDHB | Lactate dehydrogenase B | 12 | 21679543 | 21702043 | − | −2.32 | 6.4207E-04 |
LMO4 | LIM domain only 4 | 1 | 87566739 | 87587021 | + | −2.42 | 1.3021E-03 |
LOC124220 | Similar to common salivary protein 1 | 16 | 2820174 | 2822285 | + | 3.78 | 4.8845E-04 |
LOC391271 | Hypothetical LOC391271 | 21 | 20719132 | 20720350 | − | 2.65 | 9.3351E-05 |
MAML2 | Mastermind-like 2 (Drosophila) | 11 | 95349407 | 95355511 | − | −2.14 | 1.0648E-02 |
MID1 | Midline 1 (Opitz/BBB syndrome) | 1 | 145841560 | 145848017 | + | −2.07 | 2.1773E-02 |
MMP7 | Matrix metallopeptidase 7 (matrilysin, uterine) | 11 | 101896450 | 101906688 | − | −2.85 | 7.1351E-03 |
PRAME | Preferentially expressed antigen in melanoma | 22 | 21220124 | 21231696 | − | −4.30 | 4.3286E-04 |
PSAT1 | Phosphoserine aminotransferase 1 | 9 | 80101879 | 80134827 | + | −2.11 | 3.2517E-03 |
REEP5 | Receptor accessory protein 5 | 5 | 112239980 | 112285930 | − | 2.04 | 6.4207E-04 |
RP5-860F19.3 | Early B-cell factor 4 | 20 | 2612040 | 2688754 | + | 2.02 | 8.3191E-03 |
RTN4RL1 | Reticulon 4 receptor-like 1 | 17 | 1786540 | 1787865 | − | 2.28 | 6.4207E-04 |
SCUBE2 | Signal peptide, CUB domain, EGF-like 2 | 11 | 8998511 | 9069731 | − | 4.13 | 3.3991E-05 |
SLITRK6 | SLIT and NTRK-like family, member 6 | 13 | 85264923 | 85271484 | − | 3.57 | 6.4207E-04 |
STARD10 | StAR-related lipid transfer (START) domain containing 10 | 11 | 72143422 | 72182398 | − | 3.16 | 3.2803E-04 |
TFF1 | Trefoil factor 1 | 21 | 42655462 | 42659713 | − | 3.38 | 1.3021E-03 |
TMEM16A | Transmembrane protein 16A | 11 | 69602056 | 69713281 | + | 2.24 | 6.1384E-03 |
TNFRSF21 | Tumor necrosis factor receptor superfamily, member 21 | 6 | 47307227 | 47385321 | − | −2.07 | 1.6305E-03 |
TSPAN13 | Tetraspanin 13 | 7 | 16785818 | 16789424 | + | 2.34 | 1.1854E-02 |
UBD | Ubiquitin D | 6 | 29667268 | 29671562 | − | −2.27 | 2.9004E-02 |
