Table 3

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


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

a Calculated by TTEST (equal variance, 2-tailed distribution).

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.

Park and Stegall BMC Genomics 2007 8:88   doi:10.1186/1471-2164-8-88