Skip to main content

Table 3 Real-time RT-PCR analysis of significant genes (p < 0.05) identified in microarray data normalized with and/or without EC dilution series.

From: Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™

Name

Full Name

GenBank

Overall Treatment Effect

Pairwise Comparisons

   

With EC

Without EC

# of Flagged Spots

 

With EC

Without EC

RT-PCR

   

p-value

p-value

Sample

Ref.

Comparison

foldchange

p-value

foldchange

p-value

foldchange

p-value

Differentially expressed using both the EC and non-EC normalization

Adcy6

adenylate cyclase 6

NM_007405

0.0004

0.0068

6

0

100 mg/kg

-1.43

0.0003

-1.34

0.0037

  

Chk

choline kinase

NM_013490

0.0039

0.0223

1

0

100 mg/kg

-1.45

0.0041

-1.39

0.0214

-2.39

0.0122

Cyp2b10

Cytochrome P450, 2b10, phenobarbitol inducible, type b

NM_009998

0.0000

0.0000

8

20

100 mg/kg

5.10

0.0000

3.93

0.0000

3.76

0.0001

Cyp2b10

 

NM_009998

    

10 mg/kg

2.95

0.0000

2.92

0.0000

1.04

0.8600

Cyp2b9

cytochrome P450, 2b9, phenobarbitol inducible, type a

NM_010000

0.0000

0.0000

15

22

100 mg/kg

8.29

0.0000

8.55

0.0000

3.04

0.0965

Cyp2b9

 

NM_010000

    

10 mg/kg

3.22

0.0000

3.56

0.0000

2.74

0.0052

Ephx1

epoxide hydrolase 1, microsomal; Eph1, Eph-1, AI195553

NM_010145

0.0181

0.0021

0

0

100 mg/kg

1.33

0.0486

1.39

0.0004

1.46

0.0350

Gadd45a

growth arrest and DNA damage inducible

NM_007836

0.0000

0.0000

17

0

100 mg/kg

1.66

0.0003

1.62

0.0024

  

Gadd45b

growth arrest and DNA-damage-inducible 45 beta

NM_008655

0.0000

0.0000

25

1

100 mg/kg

1.92

0.0000

1.93

0.0000

  

Gdf15

growth differentiation factor 15

NM_011819

0.0000

0.0002

10

1

100 mg/kg

2.83

0.0000

2.57

0.0000

  

gstm2

glutathione S-transferase, mu 2

NM_008183

0.0054

0.0002

0

0

100 mg/kg

1.39

0.0313

1.40

0.0000

1.50

0.0013

Gstm3

glutathione S-transferase, mu 3

J03953

0.0000

0.0160

6

24

100 mg/kg

2.16

0.0000

2.21

0.0131

  

Lbp

Lipopolysaccharide binding protein

NM_008489

0.0379

0.0051

1

25

100 mg/kg

1.39

0.0104

1.38

0.0037

1.60

0.0345

Lpin1

lipin 1

NM_015763

0.0039

0.0037

0

3

100 mg/kg

-1.94

0.0009

-1.66

0.0037

  

Differentially expressed using EC normalization only

AhR

rat Ah receptor

NM_013464

0.0039

0.0436

0

0

100 mg/kg

1.48

0.0423

1.42

0.0676

2.03

0.0003

Mpg

N-methylpurine-DNA glycosylase

NM_010822

0.041698

0.3782

25

25

10 mg/kg

1.30

0.0420

1.13

0.3911

1.42

0.0096

Olfr1161

olfactory receptor 1161

NM_146848

0.03003

0.0800

25

25

10 mg/kg

1.30

0.0420

1.12

0.3921

1.02

0.9618

sult1c2

sulfotransferase family 1C, member 2

NM_026935

0.0350

0.0572

18

25

100 mg/kg

1.55

0.0044

1.56

0.0214

1.60

0.0161

Tieg1

TGFB inducible early growth response 1

NM_013692

0.0062

0.1318

0

0

100 mg/kg

-1.64

0.0011

-1.45

0.0627

-2.88

0.0008

Ube2b

ubiquitin conjugating enzyme

NM_009458

0.0350

0.0897

0

0

100 mg/kg

-1.23

0.0358

-1.16

0.7402

-1.56

0.0058

Differentially expressed using non-EC normalization only

cd8b

CD8 antigen, beta chain

NM_009858

0.2327

0.0436

25

25

100 mg/kg

-1.10

0.8557

-1.16

0.0158

1.40

0.3272

Dusp6

dual specificity phosphatase 6

NM_026268

0.0181

0.0107

16

0

100 mg/kg

1.39

0.0852

1.41

0.0486

1.40

0.0752

Gsta2

Glutathione S-transferase, alpha 2 (Yc2)

NM_008182

0.0681

0.0160

0

0

100 mg/kg

1.84

0.2849

2.26

0.0353

4.02

0.0026

Gsta4

Glutathione S-transferase, alpha 4

NM_010357

0.0045

0.0006

4

4

100 mg/kg

1.32

0.1312

1.41

0.0037

1.20

0.2200

Idi1

isopentenyl-diphosphate delta isomerase

NM_145360

0.0835

0.0436

0

0

100 mg/kg

-1.58

0.1234

-1.57

0.0254

-1.16

0.3523

Pitpn

phosphatidylinositol transfer protein

NM_008850

0.0969

0.0004

20

15

100 mg/kg

1.24

0.0624

1.23

0.0000

1.07

0.3100

Por

NADPH cytochrome p450 oxidoreductase

NM_008898

0.0402

0.0341

0

0

100 mg/kg

1.66

0.0806

1.55

0.0489

1.45

0.0064

Rbp1

retinol binding protein 1, cellular

NM_011254

0.0101

0.0094

0

7

100 mg/kg

1.34

0.2364

1.49

0.0029

1.13

0.3600

Ugt1a6

UDP glycosyltransferase 1 family, polypeptide A6

XM_135531

0.0942

0.0063

0

0

100 mg/kg

1.35

0.1044

1.38

0.0019

-1.06

0.4810

Not differentially expressed

Anpep

aminopeptidase N

NM_008486

0.0070

0.0223

5

9

100 mg/kg

1.20

0.4022

1.20

0.3851

  

Anpep

 

NM_008486

    

10 mg/kg

-1.20

0.1456

-1.14

0.9253

-1.04

0.6932

Cyp2a4

Cytochrome P450, 2a4 (phenobarbitol inducer)

NM_009997

0.0818

0.0045

24

24

100 mg/kg

1.19

0.2364

1.14

0.3851

  

Cyp2a4

 

NM_009997

    

10 mg/kg

1.12

0.2511

-1.07

0.4999

1.32

0.0789

mpg

N-methylpurine-DNA glycosylase

NM_010822

0.0417

0.3782

25

25

100 mg/kg

1.09

0.8894

1.03

0.9890

-1.15

0.1757

Olfr1161

olfactory receptor 1161

NM_146848

0.0300

0.0800

25

25

100 mg/kg

1.13

0.8471

1.06

0.9867

-2.87

0.0386

Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us