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Table 2 Comparison of mean signal intensity (SI) values for the 93 gene probes between NOSE and TOV samples

From: The chemiluminescence based Ziplex® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip® expression profiles

  

Affymetrix U133A Array

Ziplex Automated Workstation

Platform Comparison

Selection Criteria1

Gene Probe

NOSE mean SI (n = 11)

TOV mean SI (n = 12)

ratio (N/T)2

ratio (T/N)2

p-value3

NOSE mean SI (n = 11)

TOV mean SI (n = 12)

ratio (N/T)2

ratio (T/N)2

p-value3

significance based on p-value3

concordance based on ratio fold-change direction

A

RGS4

291

2

181.2

0.01

<0.0001

863

41

21.1

0.05

<0.0001

agree

concordance

C

SERPINE1

1912

12

162.4

0.01

<0.0001

1426

17

82.2

0.01

<0.0001

agree

concordance

A

PDPN

57

2

23.9

0.04

0.0008

100

35

2.9

0.35

0.0023

disagree

concordance

A

ALDH1A3

661

29

22.6

0.04

0.0020

1887

76

24.8

0.04

0.0051

agree

concordance

A

IL8

1353

69

19.7

0.05

0.0151

4465

231

19.3

0.05

0.0015

agree

concordance

A

PTGIS

1470

80

18.4

0.05

<0.0001

3474

184

18.9

0.05

<0.0001

agree

concordance

A

HEG1

923

66

14.1

0.07

<0.0001

3184

252

12.6

0.08

<0.0001

agree

concordance

A

TMEM158

461

33

13.9

0.07

<0.0001

869

46

18.8

0.05

<0.0001

agree

concordance

C

CDKN1A

598

53

11.4

0.09

<0.0001

385

63

6.1

0.16

<0.0001

agree

concordance

A

CCL2

570

54

10.6

0.09

0.0010

1923

207

9.3

0.11

0.0001

agree

concordance

A

LXN

731

73

10.1

0.10

<0.0001

926

124

7.5

0.13

0.0002

agree

concordance

C

SPARC

1037

108

9.6

0.10

<0.0001

2841

341

8.3

0.12

<0.0001

agree

concordance

C

IL1B

666

70

9.6

0.10

0.0247

1559

46

34.0

0.03

0.0035

agree

concordance

A

BDKRB1

152

18

8.7

0.11

0.0004

464

22

21.0

0.05

<0.0001

agree

concordance

B

SLC16A3

425

63

6.8

0.15

<0.0001

197

37

5.3

0.19

<0.0001

agree

concordance

A

FSTL1

1837

277

6.6

0.15

<0.0001

5293

732

7.2

0.14

<0.0001

agree

concordance

C

THBS2

846

135

6.3

0.16

<0.0001

668

105

6.4

0.16

0.0009

agree

concordance

A

IGFBP4

1484

238

6.2

0.16

<0.0001

692

122

5.7

0.18

0.0001

agree

concordance

A

PTRF

976

168

5.8

0.17

<0.0001

217

77

2.8

0.35

<0.0001

agree

concordance

A

GBE1

775

136

5.7

0.18

<0.0001

988

173

5.7

0.17

<0.0001

agree

concordance

A

PLOD2

654

123

5.3

0.19

<0.0001

926

132

7.0

0.14

<0.0001

agree

concordance

A

VAT1

874

175

5.0

0.20

<0.0001

255

78

3.3

0.31

<0.0001

agree

concordance

A

COL1A1

2940

614

4.8

0.21

0.0001

1502

289

5.2

0.19

0.0003

agree

concordance

C

CCND2

324

70

4.7

0.21

0.0127

481

117

4.1

0.24

0.0337

agree

concordance

A

SELT

558

148

3.8

0.27

0.0010

166

137

1.2

0.8

>0.05

disagree

concordance

B

C1QTNF1

169

48

3.6

0.28

<0.0001

30

3

11.7

0.09

<0.0001

agree

concordance

A

VGLL3

35

10

3.5

0.29

<0.0001

75

12

6.1

0.16

0.0015

disagree

concordance

C

PGAM1

1482

473

3.1

0.32

<0.0001

1603

504

3.2

0.31

<0.0001

agree

concordance

C

TP53

55

18

3.0

0.33

0.0178

197

226

0.9

1.1

>0.05

agree

discordance

B

MSN

746

250

3.0

0.33

<0.0001

818

354

2.3

0.43

<0.0001

agree

concordance

B

PSMD3

196

66

3.0

0.34

<0.0001

735

384

1.9

0.5

<0.0001

agree

concordance

B

WSB1

300

103

2.9

0.34

0.0003

313

155

2.0

0.50

0.0006

agree

concordance

B

MRC2

313

109

2.9

0.35

<0.0001

528

138

3.8

0.26

<0.0001

agree

concordance

A

MYH10

1113

420

2.6

0.38

0.0006

1096

464

2.4

0.42

0.0106

disagree

concordance

B

NSF

180

72

2.5

0.40

<0.0001

304

170

1.8

0.6

0.0023

disagree

concordance

A

P4HB

2276

917

2.5

0.40

<0.0001

4567

1553

2.9

0.34

<0.0001

agree

concordance

C

SERPIND1

7

3

2.2

0.45

>0.05

79

117

0.7

1.5

0.0363

agree

discordance

B

RAB5C

309

142

2.2

0.46

0.0106

132

61

2.2

0.46

<0.0001

disagree

concordance

B

PFN2

800

392

2.0

0.49

<0.0001

699

444

1.6

0.6

0.0005

agree

concordance

B

TRAF4

47

23

2.0

0.50

0.0363

30

27

1.1

0.9

>0.05

agree

concordance

B

LSM12

59

31

1.9

0.5

0.0023

53

36

1.5

0.7

0.0106

agree

concordance

B

PLP2

294

157

1.9

0.5

0.0051

270

190

1.4

0.7

0.0151

agree

concordance

B

PAFAH1B1

181

98

1.9

0.5

0.0006

556

387

1.4

0.7

0.0089

disagree

concordance

B

TIMM22

42

23

1.8

0.5

0.0392

126

82

1.5

0.6

0.0001

disagree

concordance

B

AMOTL2

308

173

1.8

0.6

0.0015

776

484

1.6

0.6

0.0113

agree

concordance

B

ATP1B3

668

386

1.7

0.6

<0.0001

832

449

1.9

0.5

0.0015

disagree

concordance

C

DAPK1

181

117

1.5

0.6

>0.05

186

146

1.3

0.8

>0.05

agree

concordance

B

TFRC

894

606

1.5

0.7

0.0089

386

216

1.8

0.6

0.0062

agree

concordance

B

ATG3

200

139

1.4

0.7

0.0106

342

319

1.1

0.9

>0.05

agree

concordance

B

RNF7

177

125

1.4

0.7

0.0178

54

63

0.9

1.2

>0.05

agree

concordance

A

IL18

21

16

1.4

0.7

0.0148

125

104

1.2

0.8

0.0210

agree

concordance

C

CRKL

38

28

1.4

0.7

>0.05

18

23

0.8

1.3

>0.05

agree

concordance

B

XIST

103

76

1.4

0.7

>0.05

256

378

0.7

1.5

>0.05

agree

discordance

C

PI4KA

59

44

1.4

0.7

0.0127

110

113

1.0

1.0

>0.05

agree

concordance

D

MSH6

62

47

1.3

0.8

>0.05

227

519

0.4

2.3

0.0010

disagree

discordance

C

LZTR1

82

69

1.2

0.8

>0.05

81

74

1.1

0.9

>0.05

agree

concordance

D

MLH1

171

150

1.1

0.9

>0.05

143

150

1.0

1.0

>0.05

agree

concordance

C

MYC

151

142

1.1

0.9

>0.05

119

212

0.6

1.8

>0.05

agree

discordance

B

PCOLCE2

22

21

1.0

1.0

>0.05

39

39

1.0

1.0

>0.05

agree

concordance

C

CCND3

136

139

1.0

1.0

>0.05

101

134

0.7

1.3

0.0127

agree

concordance

D

KRAS

157

162

1.0

1.0

>0.05

150

200

0.8

1.3

>0.05

agree

concordance

A

SEPT9

880

918

1.0

1.0

>0.05

543

394

1.4

0.7

>0.05

agree

concordance

D

RB1

67

73

0.9

1.1

>0.05

166

225

0.7

1.4

>0.05

agree

concordance

D

BRCA2

10

12

0.8

1.2

>0.05

15

23

0.6

1.6

0.0210

agree

concordance

B

SNX4

43

52

0.8

1.2

>0.05

199

339

0.6

1.7

0.0042

agree

concordance

A

BTN3A2

40

48

0.8

1.2

>0.05

89

173

0.5

1.9

0.0005

disagree

concordance

C

TFF1

12

16

0.7

1.4

>0.05

226

61

3.7

0.3

<0.0001

disagree

discordance

B

NUP85

71

101

0.7

1.4

>0.05

85

134

0.6

1.6

0.0028

agree

concordance

C

JUND

759

1181

0.6

1.6

>0.05

1725

2479

0.7

1.4

>0.05

agree

concordance

B

OSBPL11

46

74

0.6

1.6

0.0151

56

148

0.4

2.6

<0.0001

disagree

concordance

D

BRCA1

15

24

0.6

1.6

>0.05

27

40

0.7

1.5

>0.05

agree

concordance

B

SR140

144

243

0.6

1.7

0.0089

13

64

0.2

5.0

<0.0001

disagree

concordance

D

BRAF

27

46

0.6

1.7

0.0089

22

47

0.5

2.1

<0.0001

disagree

concordance

C

ZNF74

12

21

0.6

1.8

0.0042

16

44

0.4

2.8

0.0002

disagree

concordance

B

TOMM70A

212

383

0.6

1.8

0.0004

115

306

0.4

2.7

<0.0001

agree

concordance

B

RPL24

1895

3503

0.5

1.8

0.0002

1834

4179

0.4

2.3

0.0003

agree

concordance

C

HSPD1

899

1682

0.5

1.9

0.0002

461

1189

0.4

2.6

0.0004

agree

concordance

D

MSH2

27

53

0.5

2.0

0.0023

112

495

0.2

4.4

<0.0001

disagree

concordance

B

MYNN

27

55

0.5

2.1

0.0001

16

40

0.4

2.5

0.0005

agree

concordance

D

ERBB2

99

230

0.4

2.3

0.0003

50

142

0.4

2.8

0.0002

agree

concordance

B

ICAM2

14

34

0.4

2.5

0.0011

13

25

0.5

1.9

0.0089

agree

concordance

B

CEP70

23

59

0.4

2.6

<0.0001

56

182

0.3

3.3

<0.0001

agree

concordance

B

TMEM97

70

195

0.4

2.8

0.0015

51

140

0.4

2.8

0.0004

disagree

concordance

B

CD300A

11

36

0.3

3.3

<0.0001

4

36

0.1

9.2

0.0006

agree

concordance

A

STAT1

30

109

0.3

3.6

0.0127

48

110

0.4

2.3

0.0210

agree

concordance

A

EVI1

11

197

0.06

17.5

<0.0001

36

636

0.06

17.5

<0.0001

agree

concordance

C

APOE

7

126

0.06

17.9

<0.0001

39

326

0.12

8.4

<0.0001

agree

concordance

A

CP

7

295

0.02

43.5

<0.0001

33

972

0.03

29.3

<0.0001

agree

concordance

A

RGS1

2

112

0.02

47.0

<0.0001

3

169

0.02

56.5

<0.0001

agree

concordance

A

SPON1

5

271

0.02

57.8

<0.0001

6

257

0.02

44.9

<0.0001

agree

concordance

A

CD24

6

481

0.01

77.2

<0.0001

63

3697

0.02

58.5

<0.0001

agree

concordance

A

IGKC

7

991

0.01

151.6

<0.0001

27

873

0.03

32.6

0.0008

agree

concordance

A

IGHG1

3

1262

0.003

374.3

<0.0001

19

203

0.10

10.5

<0.0001

agree

concordance

  1. 1See Table 1 for description of categories of selection criteria. 2Fold change >2 or <0.5 (bold) between NOSE (N) and TOV (T) gene expression comparison. 3Welch Rank Sum Test p<0.001 (italics) difference between NOSE (N) and TOV (T).
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Journal of Translational Medicine

ISSN: 1479-5876

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