Table 1.
Genes differentially expressed in HELUs versus TDLUs and ADH/DCIS versus HN tissue with a FDR < 0.1
| Gene symbol | Gene name | HELUs vs. TDLUs | ADH/DCIS vs. HN | ||
|---|---|---|---|---|---|
| Fold change (95% CI) | FDR | Fold change (95% CI) | FDR | ||
| Common between HELUs and ADH/DCIS | |||||
| EGF | Epidermal growth factor | −4.17 (ND, ND) | 0.019 | −1.04 (−1.71, −0.37) | 0.034 |
| ELF5 | E-74-like factor 5 | −2.46 (−3.60, −1.31) | 0.058 | −1.88 (−2.75, −1.00) | 0.005 |
| FOXC1 | Forkhead box C1 | −2.69 (−3.63, −1.76) | 0.023 | −0.95 (−1.38, −0.51) | 0.004 |
| JAG2 | Jagged 2 | −0.53 (−0.82, −0.23) | 0.078 | −0.92 (−1.37, −0.48) | 0.006 |
| SOX10 | SRY (sex determining region Y)-box 10 | −1.16 (−1.69, −0.64) | 0.058 | −1.38 (−1.92, −0.85) | 0.001 |
| Exclusive to HELUs | |||||
| ABCG2 | ATP-binding cassette, sub-family G, member 2 | −2.84 (−4.28, −1.39) | 0.073 | −0.62 (−1.20, −0.04) | 0.149 |
| CDC42 | Cell division cycle 42 | 0.66 (0.25, 1.07) | 0.091 | 0.99 (−0.12, 0.31) | 0.914 |
| CLDN10 | Claudin 10 | −2.70 (−4.52, −1.06) | 0.091 | 0.33 (−0.26, 0.93) | 0.864 |
| EPCAM | Epithelial cell adhesion molecule | 0.88 (0.60, 1.17) | 0.019 | 0.14 (−0.42, 0.69) | 0.928 |
| EZH1 | Enhancer of zeste homolog 1 | −0.74 (−1.12, −0.35) | 0.073 | 0.12 (−0.35, 0.58) | 0.928 |
| FOXA1 | Forkhead box A1 | 2.03 (1.05, 3.00) | 0.064 | 0.48 (−0.28, 1.25) | 0.855 |
| HOXB2 | Homeobox B2 | 1.83 (1.40, 2.26) | 0.008 | −0.07 (−0.72, 0.58) | 0.959 |
| HOXC10 | Homeobox C10 | 1.09 (ND, ND) | 0.091 | 0.22 (−0.30, 0.74) | 0.914 |
| HOXC11 | Homeobox C11 | 3.03 (1.22, 4.84) | 0.091 | 0.13 (−0.15, 0.42) | 0.913 |
| IL7R | Interleukin 7 receptor | −2.33 (−3.75, −0.90) | 0.091 | 0.23 (−0.38, 0.84) | 0.914 |
| ITGA6 | Integrin, alpha 6 | −0.85 (−1.28, −0.41) | 0.073 | −0.27 (−1.15, 0.60) | 0.914 |
| ITGB1 | Integrin, beta 1 | −0.82 (−1.17, −0.48) | 0.049 | 0.58 (0.12, 1.04) | 0.830 |
| ITGB4 | Integrin, beta 4 | −0.81 (−1.23, −0.38) | 0.073 | −0.02 (−0.34, 0.30) | 0.960 |
| MFGE8 | Milk fat globule-EGF factor 8 | −1.19 (−1.87, −0.52) | 0.078 | −0.20 (−0.60, 0.20) | 0.899 |
| MLL4 | Myeloid/lymphoid or mixed-lineage leukemia 4 | −0.61 (−0.99, −0.22) | 0.092 | 0.04 (−0.60, 0.68) | 0.960 |
| MYC | v-Myc myelocytomatosis viral oncogene homolog (avian) | −2.85 (−4.46, −1.24) | 0.078 | −0.45 (−1.19, 0.28) | 0.855 |
| NOTCH3 | Notch homolog 3 | −0.49 (−0.76, −0.23) | 0.077 | 0.04 (−0.22, 0.30) | 0.959 |
| PGR | Progesterone receptor | 2.46 (1.49, 3.42) | 0.038 | 0.13 (−1.21, 1.46) | 0.959 |
| PROM1 | Prominin 1 | −3.17 (−4.98, −1.36) | 0.078 | −0.78 (−1.96, 0.40) | 0.849 |
| SMARCA4 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 | −0.77 (−1.21, −0.34) | 0.078 | 0.11 (−0.20, 0.42) | 0.914 |
| SOX9 | SRY (sex determining region Y)-box 9 | −2.45 (−3.58, −1.31) | 0.058 | −0.26 (−1.01, 0.49) | 0.914 |
| TGFA | Transforming growth factor, alpha | −1.50 (−2.41, −0.58) | 0.091 | −0.08 (−0.42, 0.25) | 0.928 |
| TGFB2 | Transforming growth factor, beta 2 | −1.04 (ND, ND) | 0.092 | −0.14 (−0.71, 0.42) | 0.928 |
| Exclusive for ADH/DCIS | |||||
| ACTA2 | Actin, alpha 2 | −0.32 (−0.71, 0.06) | 0.353 | −2.25 (−2.95, −1.55) | 0.0001 |
| AKT1 | v-Akt murine thymoma viral oncogene homolog 1 | 0.21 (−0.65, 1.08) | 0.798 | 1.07 (0.41, 1.72) | 0.029 |
| CBX8 | Chromobox homolog 8 | −0.82 (−1.55, −0.08) | 0.207 | −0.97 (−1.58, −0.37) | 0.029 |
| CD24 | CD24 molecule | 0.29 (−0.89, 1.46) | 0.799 | 0.65 (0.34, 0.95) | 0.006 |
| CLDN7 | Claudin 7 | 0.24 (ND, ND) | 0.789 | 0.49 (0.17, 0.82) | 0.036 |
| EGFR | Epidermal growth factor receptor | −0.65 (−1.20, −0.09) | 0.184 | −0.62 (−0.90, −0.34) | 0.004 |
| EZH2 | Enhancer of zeste homolog 2 | 0.90 (−0.31, 2.12) | 0.412 | 1.61 (0.87, 2.34) | 0.004 |
| GATA3 | GATA-binding protein 3 | 1.12 (ND, ND) | 0.136 | 0.95 (0.47, 1.43) | 0.008 |
| HOXA4 | Homeobox A4 | −1.13 (−1.92, −0.35) | 0.123 | −0.64 (−1.05, −0.22) | 0.036 |
| HOXA5 | Homeobox A5 | −1.40 (−2.61, −0.18) | 0.189 | −1.93 (−2.50, −1.35) | 0.0001 |
| HOXA7 | Homeobox A7 | −1.54 (−2.78, −0.29) | 0.174 | −0.77 (−1.14, −0.40) | 0.006 |
| HOXA9 | Homeobox A9 | NA | NA | −3.31 (−4.66, −0.96) | 0.002 |
| HOXB6 | Homeobox B6 | 0.74 (ND, ND) | 0.685 | 0.92 (0.32, 1.52) | 0.075 |
| ID2 | Inhibitor of DNA-binding 2 | −0.34 (−1.31, 0.64) | 0.699 | 0.59 (0.21, 0.96) | 0.063 |
| JAM2 | Junctional adhesion molecule 2 | −0.62 (−2.06, 0.82) | 0.638 | −0.91 (−1.32, −0.49) | 0.004 |
| JAM3 | Junctional adhesion molecule 3 | −0.55 (−1.58, 0.49) | 0.566 | −1.09 (−1.50, −0.68) | 0.001 |
| KRT17 | Keratin 17 | 0.06 (−0.65, 0.77) | 0.948 | −1.63 (−2.56, −0.71) | 0.013 |
| MME | Membrane metallo-endopeptidase | −0.44 (−1.35, 0.46) | 0.611 | −4.42 (−5.58, −3.25) | <0.001 |
| PDGFA | Platelet-derived growth factor receptor, alpha polypeptide | −0.98 (−1.77, −0.18) | 0.174 | −1.28 (−1.94, −0.63) | 0.008 |
| SNAI2 | Snail homolog 2 | −0.65 (−1.58, 0.29) | 0.439 | −1.79 (−2.59, −0.99) | 0.004 |
| TGFBR3 | Transforming growth factor receptor, beta 3 | −0.85 (−1.65, −0.05) | 0.229 | −2.02 (−3.09, −0.96) | 0.010 |
| TJP3 | Tight junction protein 3 | −0.47 (−0.99, 0.04) | 0.294 | 1.13 (0.51, 1.76) | 0.013 |
| WNT5B | Wingless-type MMTV integration site family, member 5B | 0.21 (−0.86, 1.27) | 0.864 | −2.71 (−3.75, −1.66) | 0.001 |
HELU, hyperplastic enlarged lobular unit; TDLU, terminal duct lobular unit; ADH, atypical ductal hyperplasia; DCIS, ductal carcinoma in situ; HN, histologically normal; FDR, false discovery rate; CI, confidence interval; vs., versus; ND, not determined; NA, probe set not available on HG-U133A Human GeneChip microarray.