Table 4. DESeq results showing significant changes of gene expression in subtype- or stage-matched AA tumors.
| Gene | Stage/Subtype | Log2 Fold-Change | P-value | P-adj | Relevance | Citation |
|---|---|---|---|---|---|---|
| TARP | HER2 | 8.74 | 2.31E-04 | 5.01E-01 | Breast and prostate tumor-associated antigen | [40] |
| PKDREJ | Luminal A | -1.18 | 9.56E-04 | 4.20E-01 | Point mutated in breast cancers | [39] |
| PGLYRP1 | Triple negative | 2.99 | 7.64E-04 | 1.00E+00 | Increased in expression may reflect immune cell response to developing breast tumor | [41] |
| BUB1 | Stage I | 1.05 | 9.80E-04 | 7.44E-01 | Nuclear localization is a potent prognostic factor for human breast cancer | [36] |
| GALNT6 | Stage I | -1.45 | 3.00E-04 | 4.03E-01 | Deregulation of GALNT6 gene could be an early event during human breast carcinogenesis | [81] |
| CRYBB2 | Stage II | 2.00 | 3.27E-10 | 6.60E-06 | Differentially expressed in several studies investigating cancer health disparity | [19,20,37,38] |
| FLJ45983 | Stage III | -2.40 | 2.21E-04 | 5.66E-02 | Putative uncharacterized protein; Hypermethylated in primary and metastatic tumors | [82] |
| ESR1 | Stage III | -2.25 | 8.80E-05 | 4.91E-02 | Estrogen receptor alpha | |
| FOXA1 | Stage III | -1.15 | 3.48E-05 | 3.97E-02 | Expression correlates with luminal subtype A breast cancer; significant predictor of cancer-specific survival in patients with ER-positive tumors | [83] |
| LRIG1 | Stage III | -1.10 | 3.39E-04 | 6.11E-02 | Estrogen-regulated growth suppressor; correlates with longer relapse-free survival in ERα-positive breast cancer; tumor suppressor | [84,85] |
| PLCG2 | Stage III | 1.00 | 1.08E-04 | 4.91E-02 | Hypermethylated in metastatic breast cancer cell line | [86] |
Log2 fold-change is for mean AA expression relative to mean CA expression. Log2-fold change is calculated as log2(AA/CA). Bold entries have been previously observed as differentially expressed in literature. Gene names: CRYBB2 - crystallin, beta B2; CYP4F8 - cytochrome P450, family 4, subfamily F, polypeptide 8; ESR1 - estrogen receptor 1; FLJ45983 - Not Available; FOXA1 - forkhead box A1; GALNT6 - UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6); LRIG1 - leucine-rich repeats and immunoglobulin-like domains 1; PGLYRP1 - peptidoglycan recognition protein 1; PKDREJ - polycystin (PKD) family receptor for egg jelly; PLCG2 - phospholipase C, gamma 2 (phosphatidylinositol-specific), TARP - TCRgamma alternative reading frame protein.