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Table 3 Example of genes with significant main effects

From: Analysis of oligonucleotide array experiments with repeated measures using mixed models

Gene

 

Log2 based data

Overall P-value

Interaction P-value

Main effect of Disease

Main effect of Region

  

OB

CER

  

P value

fold

dir

P value

fold

dir

 

Con

12.68

12.73

12.83

12.37

12.34

12.53

        
  

12.75 ± 0.08

12.41 ± 0.10

        

HMGN2

       

0.0003

0.6462

0.0009*

0.63

D

0.011†

1.24

N

 

AD

12.01

11.94

12.16

11.53

12.04

11.81

        
  

12.04 ± 0.11

11.79 ± 0.26

        
 

Con

10.44

10.22

10.26

10.09

10.16

9.80

        
  

10.31 ± 0.12

10.02 ± 0.19

        

TSG101

       

0.0002

0.0726

0.0021*

1.51

I

0.056

1.42

N

 

AD

11.20

11.01

10.96

10.30

10.59

10.34

        
  

11.06 ± 0.13

10.41 ± 0.16

        
 

Con

11.49

10.91

10.83

12.56

12.47

12.62

        
  

11.08 ± 0.36

12.55 ± 0.08

        

RELN

       

0.0025

0.8328

0.5004

0.92

N

0.0005*

0.37

D

 

AD

11.33

11.00

10.66

12.45

12.35

12.41

        
  

11.00 ± 0.34

12.41 ± 0.06

        
 

Con

14.01

14.54

13.89

13.21

13.34

12.74

        
  

14.15 ± 0.35

13.10 ± 0.32

        

B2M

       

0.0011

0.3767

0.5986

0.94

N

0.0002*

2.20

I

 

AD

14.03

13.84

14.47

12.70

12.88

13.06

        
  

14.11 ± 0.32

12.88 ± 0.18

        
  1. * indicates the P values pass the FDR 5% criteria. † indicates the P values are smaller than 0.05 but larger than the critical value 0.0033 determined by the FDR procedure. Overall P-value and interaction P-value are the same with the Overall P and Interaction P in Table 4. P values of main effect of disease and region are the P values of Type III ANOVA test using proc mixed procedure in SAS. Fold of main effect of disease: the ratio of the average intensities of AD (average over OB and CER) over Control (average over OB and CER). Fold of main effect of region: the ratio of the average intensities of OB (average over Control and AD) over CER (average over Control and AD). See also Figure 1.