Table 3 Comparison of gene expression in copy number neutral (CNN) genes with LOH and without LOH (normal) (N = 46 genes significantly differentially-expressed 2-fold or greater)*

ADK

chr10q22|10q11-q24

204120_s_at

2

13

46

0.404

0.606

3.138

8.559E-03

ADK

chr10q22|10q11-q24

204119_s_at

2

13

46

0.411

0.619

3.195

7.278E-03

AIM1L

chr1p36.11

220289_s_at

2

15

6

0.093

0.201

3.548

4.812E-03

APOL6

chr22q12.3

219716_at

2

5

4

0.467

0.894

4.659

9.543E-03

ATP6V0E1

chr5q35.2

201171_at

2

12

5

0.375

0.669

3.234

9.843E-03

ATP6V0E1

chr5q35.2

200096_s_at

2

12

5

0.480

0.872

4.445

5.699E-03

BACH1

chr21q22.11

204194_at

2

12

9

0.498

0.738

3.970

2.098E-03

BTG2

chr1q32

201236_s_at

2

14

1

0.460

0.986

4.095

1.183E-03

CD2

chr1p13.1

205831_at

2

14

1

0.324

0.628

3.462

9.221E-03

CEACAM6

chr19q13.2

211657_at

2

13

3

0.007

0.100

4.779

7.023E-03

CRAT

chr9q34.1

209522_s_at

7

8

1

0.293

0.567

3.169

7.495E-03

CSDE1

chr1p22

202646_s_at

2

14

3

0.343

0.895

7.835

7.590E-05

CYP4F3

chr19p13.2

206515_at

2

13

136

0.065

0.307

3.329

5.631E-03

DIO2

chr14q24.2-q24.3

203699_s_at

2

11

4

0.072

0.127

3.565

6.175E-03

DIO2

chr14q24.2-q24.3

203700_s_at

2

11

4

0.168

0.280

3.697

3.752E-03

EIF4EBP2

chr10q21-q22

208770_s_at

2

14

1

0.452

0.657

6.300

2.692E-05

FAS

chr10q24.1

216252_x_at

2

13

8

0.412

0.648

3.058

9.883E-03

HERC6

chr4q22.1

219352_at

3

9

1

0.105

0.538

5.769

2.901E-04

ICAM3

chr19p13.3-p13.2

204949_at

2

13

2

0.356

0.602

3.478

4.342E-03

IL1RN

chr2q14.2

212659_s_at

2

12

13

0.073

0.142

3.256

7.793E-03

NADSYN1

chr11q13.4

218840_s_at

2

8

10

0.448

0.649

3.399

9.384E-03

NHP2

chr5q35.3

216583_x_at

2

10

1

0.497

0.774

4.091

2.584E-03

PDCD4

chr10q24

202730_s_at

2

12

4

0.212

0.363

4.483

9.256E-04

PPP1R13L

chr19q13.32

218849_s_at

3

13

1

0.190

0.487

5.016

5.018E-04

RIPK4

chr21q22.3

221215_s_at

5

10

7

0.217

0.454

3.614

3.658E-03

SKAP2

chr7p21-p15

216899_s_at

2

10

12

0.293

0.615

4.165

1.973E-03

SKAP2

chr7p21-p15

204361_s_at

2

10

43

0.359

0.665

4.384

1.591E-03

SLC6A1

chr3p25-p24

205152_at

2

8

6

0.158

0.438

5.044

2.481E-03

STK39

chr2q24.3

202786_at

2

12

86

0.151

0.290

3.363

6.327E-03

SYNPO2L

chr10q22.2

219804_at

3

13

1

0.063

0.345

6.925

8.703E-06

TGM5

chr15q15.2

207911_s_at

2

13

8

0.382

0.517

3.496

4.389E-03

ZNF91

chr19p13.1-p12

206059_at

2

10

5

0.026

0.551

9.054

6.430E-04

ACVR1

chr2q23-q24

203935_at

2

12

13

3.480

1.751

-4.533

7.869E-04

ASPN

chr9q22

219087_at

5

10

2

10.594

2.679

-3.792

2.667E-03

BUB1

chr2q14

209642_at

2

12

2

8.571

4.010

-3.922

2.170E-03

CALU

chr7q32.1

200757_s_at

2

12

7

3.467

1.830

-4.612

7.505E-04

CALU

chr7q32.1

200755_s_at

2

12

7

3.899

1.981

-3.903

2.269E-03

CAMSAP1L1

chr1q32.1

212765_at

2

13

3

3.000

1.357

-6.288

1.629E-03

CENPF

chr1q32-q41

209172_s_at

2

14

10

5.481

2.643

-5.909

3.926E-05

CSNK1E

chr22q13.1

202332_at

2

3

4

2.933

1.157

-7.434

9.278E-03

FAM13A

chr4q22.1

202973_x_at

3

10

14

2.756

1.149

-3.508

6.115E-03

FHL2

chr2q12-q14

202949_s_at

2

14

15

3.159

1.244

-4.697

4.097E-04

GSR

chr8p21.1

205770_at

3

10

8

2.505

1.222

-3.701

4.824E-03

ITGA6

chr2q31.1

201656_at

2

11

21

4.038

2.400

-3.519

4.820E-03

KIF14

chr1q32.1

206364_at

2

13

6

11.027

3.578

-8.257

2.071E-06

NCAPH

chr2q11.2

212949_at

2

11

2

3.643

1.943

-5.087

4.450E-04

NRP2

chr2q33.3

214632_at

3

11

29

2.161

1.257

-3.500

9.276E-03

RBM28

chr7q32.1

218593_at

2

11

9

2.210

1.555

-3.976

2.370E-03

SMAD5

chr5q31

205187_at

2

12

3

2.208

0.829

-10.692

3.171E-07

STEAP3

chr2q14.2

218424_s_at

2

14

12

2.707

1.207

-6.922

9.985E-06

TGS1

chr8q11

219231_at

2

8

1

2.533

1.656

-3.495

8.601E-03