Table 3 Replicated in- cis miRNAs and associations with clinical parameters
| Â | miRNA | Chromosomal location (hg19) | Direction | Associated miRNA aberration | P-value (FDR-corrected, discovery cohort) | P-value (FDR-corrected, replication cohort) |
|---|---|---|---|---|---|---|
TP53 status (wild-type versus mutant) | miR-19a-3p | 13q31.3 | Up in TP53 mutated samples | Hypomethylation | 7.5E-03 | 9.1E-03 |
Grade (1, 2 and 3) | miR-30c-2-3p | 6q13 | Decreasing with grade | Hypomethylation | 1.7E-02 | 2.8E-02 |
| Â | miR-93-5p | 7q22.1 | Increasing with grade | Gain | 4.4E-03 | 4.2E-02 |
ER status (positive (+) versus negative (-)) | miR-9-3p | 15q26.1 | Down in ER+/up in ER- | Gain | 9.0E-04 | 4.1E-03 |
| Â | miR-17-5p | 13q31.3 | Down in ER+/up in ER- | Hypomethylation | 1.5E-02 | 2.9E-03 |
| Â | miR-19a-3p | 13q31.3 | Down in ER+/up in ER- | Hypomethylation | 2.9E-02 | 2.1E-05 |
| Â | miR-93-5p | 7q22.1 | Down in ER+/up in ER- | Gain | 3.8E-02 | 2.7E-02 |
| Â | miR-130b-3p | 22q11.21 | Down in ER+/up in ER- | Gain | 3.5E-02 | 5.0E-02 |
| Â | miR-30c-2-3p | 6q13 | Up in ER+/down in ER- | Hypomethylation | 4.9E-02 | 2.4E-02 |
| Â | miR-125a-5p | 19q13.41 | Up in ER+/down in ER- | Hypermethylation | 1.1E-02 | 3.1E-03 |
| Â | miR-190b | 1q21.3 | Up in ER+/down in ER- | Hypomethylation | 3.5E-07 | 3.0E-02 |
Luminal versus basal-like subtype | miR-125a-5p | 19q13.41 | Up in luminal/down in basal-like | Hypermethylation | 6.4E-03 | 1.3E-03 |
| Â | miR-148b-3p | 12q13.13 | Up in luminal/down in basal-like | Gain | 1.6E-05 | 1.0E-02 |
| Â | miR-190b | 1q21.3 | Up in luminal/down in basal-like | Hypomethylation | 1.6E-05 | 1.7E-04 |
| Â | miR-193b-3p | 16p13.12 | Up in luminal/down in basal-like | Gain | 2.5E-04 | 4.0E-06 |
| Â | let-7e-3p | 19q13.41 | Up in luminal/down in basal-like | Hypermethylation | 1.5E-02 | 8.3E-03 |
| Â | miR-9-3p | 15q26.1 | Down in luminal/up in basal-like | Gain | 2.4E-05 | 4.9E-03 |
| Â | miR-17-3p | 13q31.3 | Down in luminal/up in basal-like | Hypomethylation | 2.5E-05 | 1.9E-04 |
| Â | miR-17-5p | 13q31.3 | Down in luminal/up in basal-like | Hypomethylation | 1.8E-04 | 1.2E-04 |
| Â | miR-19b-3p | 13q31.3 | Down in luminal/up in basal-like | Hypomethylation | 2.8E-05 | 4.0E-06 |
| Â | miR-19a-3p | 13q31.3 | Down in luminal/up in basal-like | Hypomethylation | 1.4E-04 | 4.0E-06 |
| Â | miR-135b-5p | 1q32.1 | Down in luminal/up in basal-like | Hypomethylation | 1.6E-05 | 2.8E-03 |
| Â | miR-142-5p | 17q22 | Down in luminal/up in basal-like | Hypomethylation | 8.6E-03 | 1.4E-02 |