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

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

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

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