Table 3

Example of genes with significant main effects
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







* 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.

Li et al. BMC Bioinformatics 2004 5:209   doi:10.1186/1471-2105-5-209