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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