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Table 3 Comparisons of changes in gene expression determined by microarray and rt-PCR in Mayo Clinic kidney transplant specimens.

From: A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

   RT-PCR Microarray  
Transcript Analysis Fold change p-valuea Fold change p-value %P Acceptable correlationb
A. Undetectable by microarray
TNFα        
  TxNormal (0–12) 1.62 0.288 -1.05 0.051 0% No
  TxFibrosis (0–12) 2.05 0.061 -1.01 0.728 0% No
IFNγ        
  TxNormal (0–12) 2.72 0.172 -1.04 0.152 0% No
  TxFibrosis (0–12) 3.11 0.028 1.02 0.537 0% No
IL-10        
  TxNormal (0–12) 1.54 0.271 -1.05 0.058 0% No
  TxFibrosis (0–12) 3.02 0.000 -1.05 0.134 0% No
TGFβ1        
  TxNormal (0–12) 2.53 0.003 -1.11 0.012 0% No
  TxFibrosis (0–12) 2.93 0.000 -1.09 0.002 0% No
Fox-P3        
  TxNormal (0–12) 2.56 0.030 -1.07 0.029 0% No
  TxFibrosis (0–12) 2.33 0.000 -1.13 0.001 0% No
B. Detectable by microarray
GRZMA        
  TxNormal (0–12) 7.25 0.021 1.32 0.072 42% No
  TxFibrosis (0–12) 9.21 0.000 2.06 0.000 50% Yes
IL-6        
  TxNormal (0–12) -12.50 0.029 -1.26 0.008 79% Yes
  TxFibrosis (0–12) -7.69 0.005 -1.23 0.000 63% Yes
FN1        
  TxNormal (0–12) 2.84 0.001 2.78 0.020 93% Yes
  TxFibrosis (0–12) 2.50 0.002 2.01 0.001 94% Yes
IFNγ-R1        
  TxNormal (0–12) 1.45 0.072 1.35 0.061 100% Yes
  TxFibrosis (0–12) 1.63 0.001 1.37 0.008 100% Yes
IER3        
  TxNormal (0–12) -2.80 0.016 -2.54 0.000 100% Yes
  TxFibrosis (0–12) -2.24 0.005 -1.70 0.000 100% Yes
STAT2        
  TxNormal (0–12) 1.72 0.015 1.40 0.005 100% Yes
  TxFibrosis (0–12) 1.88 0.016 1.43 0.001 100% Yes
COL1A1        
  TxNormal (0–12) 8.89 0.037 5.82 0.005 100% Yes
  TxFibrosis (0–12) 8.76 0.001 5.34 0.000 100% Yes
STAT1        
  TxNormal (0–12) 2.06 0.001 1.89 0.000 100% Yes
  TxFibrosis (0–12) 2.80 0.002 2.19 0.000 100% Yes
VCAM1        
  TxNormal (0–12) 1.42 0.168 1.34 0.254 100% Yes
  TxFibrosis (0–12) 2.43 0.000 2.00 0.000 100% Yes
PSMB8        
  TxNormal (0–12) 1.78 0.019 1.40 0.041 100% Yes
  TxFibrosis (0–12) 2.82 0.000 1.83 0.000 100% Yes
  1. a Calculated by TTEST (equal variance, 2-tailed distribution).
  2. b To be considered "acceptable" both the direction of change (up/down- regulation) and significance (p < 0.05 or p > 0.05) must be the same.