Table 1.
Comparison between normal, DCIS and IDC specimens using EdgeR.
| miRNA levels in carcinomas | miRNA genomic cluster | Normal (rf) | DCIS (rf) | HER2 positive IDC (rf) | Normal vs DCIS fold change (p value) | Normal vs HER2 positive IDC fold change (p value) | DCIS vs HER2 positive IDC fold change (p value) |
|---|---|---|---|---|---|---|---|
| Downregulated miRNAs | |||||||
| sf-miR-22 (1) | cluster-mir-22 (1) | 0.120 | 0.033 | 0.042 | 3.7 (0.0006) | 2.9 (0.0008) | 0.8 (1) |
| sf-miR-125a (3) | cluster-mir-98 (13) | 0.088 | 0.029 | 0.013 | 3.1 (0.007) | 6.8 (1.3E-13) | 2.2 (0.02) |
| sf-miR-99a (3) | cluster-mir-98 (13) | 0.066 | 0.018 | 0.015 | 3.6 (0.0008) | 4.5 (3.9E-08) | 1.2 (1) |
| sf-let-7a-1 (12) | cluster-mir-98 (13) | 0.148 | 0.076 | 0.120 | 2.0 (1) | 1.2 (1) | 0.6 (1) |
| sf-miR-451-DICER1 (1) | cluster-mir-144 (2) | 0.053 | 0.009 | 0.004 | 5.7 (2.4E-07) | 11.8 (8.8E-23) | 2.1 (0.06) |
| sf-miR-144 (1) | cluster-mir-144 (2) | 0.003 | 0.001 | 0.000 | 2.6 (0.067) | 7.0 (5.67E-14) | 2.7 (0.0005) |
| sf-miR-145 (1) | cluster-mir-143(2) | 0.046 | 0.015 | 0.009 | 3.1 (0.006) | 4.9 (3.0E-09) | 1.6 (1) |
| sf-miR-143(1) | cluster-mir-143(2) | 0.042 | 0.043 | 0.022 | 1.0 (1) | 1.9 (0.559) | 1.9 (0.130) |
| sf-miR-143*(1) | cluster-mir-143(2) | 0.008 | 0.001 | 0.001 | 8.0 (4.48E-10) | 7.9 (6.54E-16) | 1.0 (1) |
| sf-miR-320-RNASEN(1) | cluster-mir-320-RNASEN(1) | 0.036 | 0.006 | 0.005 | 6.5 (2.5E-08) | 7.7 (1.2E-15) | 1.2 (1) |
| sf-miR-378(1) | cluster-mir-378(1) | 0.022 | 0.004 | 0.003 | 5.7 (3.3E-07) | 8.5 (4.6E-17) | 1.5 (1) |
| sf-miR-497(1) | cluster-mir-195(2) | 0.011 | 0.003 | 0.003 | 4.3 (0.00004) | 4.2 (1.7E-07) | 1.0 (1) |
| sf-miR-16-1(3) | cluster-mir-195(2) | 0.002 | 0.007 | 0.006 | 0.3 (0.012) | 0.3 (0.052) | 1.3 (1) |
| Upregulated miRNAs | |||||||
| sf-miR-21(1) | cluster-mir-21(1) | 0.035 | 0.365 | 0.357 | 10.4 (2.5E-09) | 10.2 (1.4E-09) | 1.0 (1) |
| sf-miR-142-3p(1) | cluster-mir-142(1) | 0.002 | 0.003 | 0.010 | 1.5 (1) | 5.6 (0.00001) | 3.9 (8.2E-06) |
| sf-miR-142-5p(1) | cluster-mir-142(1) | 0.001 | 0.006 | 0.008 | 4.7 (0.0003) | 5.9 (7.31E-06) | 1.3 (1) |
miRNA sf expressed at >1% rf, p value ≤0.001 for at least one comparison in bold
miRNA sf that belong to same miRNA genomic cluster irrespective of expression and p values in italics