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Table 1 Genes differentially expressed in HELUs versus TDLUs and ADH/DCIS versus HN tissue with a FDR < 0.1

From: Epithelial cell identity in hyperplastic precursors of breast cancer

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
  1. 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.