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Table 1 List of genes upregulated in the microarray experiments selected for validation by qrPCR

From: A methodology for global validation of microarray experiments

Category

Affymetrix

RefSeq Title

FC Microarray*

FC PCR*

 

Probe Set ID

 

Experiment

Average

Experiment

Average

   

1

2

3

 

1

2

3

 

Top 15

          

1

104598_at

dual specificity phosphatase 1

3.96

4.52

5.37

4.58

6.93

6.74

8.36

7.31

2

98817_at

follistatin

3.20

4.43

3.83

3.79

4.88

4.92

3.65

4.44

3

93624_at

RIKEN cDNA 8430417G17

3.49

3.22

4.30

3.64

9.74

10.50

7.16

9.01

4

93319_at

RAS p21 protein activator 3

2.74

5.11

3.13

3.52

4.88

3.34

2.15

3.27

5

160894_at

CCAAT/enhancer binding protein delta

3.29

2.95

3.96

3.37

4.49

6.98

7.42

6.15

6

97844_at

regulator of G-protein signaling 2

2.79

3.83

3.00

3.17

3.65

3.21

2.70

3.16

7

160564_at

lipocalin 2

3.42

2.85

3.27

3.17

8.23

9.81

7.30

8.39

8

96346_at

cysteine dioxygenase 1, cytosolic

2.88

3.15

3.34

3.11

2.52

3.41

2.31

2.71

9

160359_at

RIKEN cDNA 1190002H23

3.06

2.65

3.18

2.95

6.20

6.14

4.23

5.44

10

92276_at

mitogen-activated protein kinase kinase kinase 6

2.75

2.89

3.14

2.92

4.27

4.95

5.42

4.86

11

101030_at

ras homolog gene family, member AB

2.81

2.38

3.77

2.93

4.93

5.82

5.56

5.42

12

102867_at

TEA domain family member 4

2.85

2.70

3.00

2.85

4.38

5.11

4.43

4.63

13

102896_at

downstream of tyrosine kinase 1

2.94

2.27

3.39

2.83

2.55

2.06

2.60

2.39

14

93573_at

metallothionein 1

2.83

2.42

2.94

2.72

3.09

3.14

3.36

3.19

15

97950_at

xanthine dehydrogenase

2.11

3.89

2.24

2.64

4.64

4.82

2.49

3.82

Stratified

          

1

160894_at

CCAAT/enhancer binding protein delta

3.29

2.95

3.96

3.37

4.49

6.98

7.42

6.15

2

102955_at

nuclear factor, interleukin 3 regulated

2.59

2.43

3.06

2.68

4.02

3.42

3.12

3.50

3

92777_at

cysteine rich protein 61

2.44

2.20

2.65

2.42

2.74

1.77

2.55

2.31

4

99027_at

Bcl2-like

2.21

1.56

2.49

2.05

2.62

1.85

2.19

2.20

5

103644_at

dipeptidase 1 (renal)

1.89

2.04

1.87

1.93

5.09

4.49

2.63

3.92

6

100952_at

stromal interaction molecule 1

1.81

1.57

1.99

1.78

2.00

1.87

1.26

1.68

7

102984_g_at

MAD homolog 1

1.56

1.68

2.07

1.75

1.23

0.95

1.15

1.11

8

161228_f_at

enabled homolog

1.69

1.61

1.57

1.62

1.68

1.43

1.42

1.51

9

103432_at

interferon-stimulated protein

1.63

1.31

1.65

1.52

1.59

1.40

1.40

1.46

10

96106_at

RIKEN cDNA 2400006P09

1.41

1.28

1.79

1.48

1.56

1.50

1.21

1.42

11

100019_at

chondroitin sulfate proteoglycan 2

1.32

1.65

1.37

1.44

1.61

1.58

1.04

1.38

12

160924_at

cDNA sequence BC028953

1.31

1.40

1.39

1.36

1.62

2.03

1.13

1.55

13

96183_at

forkhead box P1

1.34

1.28

1.31

1.31

2.06

1.68

1.52

1.74

14

103890_at

expressed sequence AW538196

1.15

1.30

1.29

1.24

1.72

0.82

2.00

1.41

15

104268_at

interleukin 6 receptor, alpha

1.18

1.20

1.19

1.19

2.75

2.08

1.48

2.04

  1. * FC is the anti-log of the average log2 FC across the three experiments; for the microarray data, a weighted (by sample size) average was calculated (n = 5 for Experiments 1 and 2 and n = 4 for Experiment 3). All microarray FCs were significant (FDR q = 0.05); all non-bolded PCR Fcs were significant (nominal p < .05).