Table 3.

Confirmation of microarray results by real-time PCR

(A) Select genes regulated by NFBD1 shRNA
Fold change NFBD1sh 0GyFold change NFBD1sh 5Gy
GenePathway(s)MicroarrayReal-time PCRMicroarrayReal-time PCR
MDC1(NFBD1)shRNA control−1.94−2.72−2.28−2.59
Cav1focal adhesion−1.52−1.63−1.55−1.61
Cav2focal adhesion−1.80−4.68−1.68−3.41
PPP1CCfocal adhesion, insulin−1.45−1.78−1.72−1.91
PTENfocal adhesion, p53−1.34−0.96−1.290.77
LAMA5focal adhesion1.00−1.44−1.58−1.23
CDH2cell adhesion molecules−1.94−1.82−2.32−1.74
STAMJak-STAT−1.51−1.82−1.51−1.74
BCL2L1Jak-STAT−1.41−1.43−1.44−0.49
IRS1Insulin−1.30−1.44−1.27−1.58
nRasInsulin−1.36−1.36−1.37−1.80
SLC2A3carbohydrate metabolism−1.41−1.46−1.33−1.58
NCBP1RNA splicing−1.66−1.57−1.48−1.89
PTBP2RNA splicing1.482.451.642.33
EIF1AXtranslation−1.63−2.04−1.51−2.38
(B) Select genes regulated by p53 shRNA
Fold change p53sh 0GyFold change p53sh 5Gy
GenePathway(s)MicroarrayReal-time PCRMicroarrayReal-time PCR
p53shRNA control−1.40−8.53−1.36−11.78
p21IR control, p53 target−1.68−2.78−2.55−0.18
(C) Select genes regulated by IR
GenePathway(s)Fold change IR
  MicroarrayReal-time PCR
p21IR control, p53 target2.434.16
AURKAIR-control, cell cycle−2.03−2.57

NOTE: Real-time PCR, using primers toward the indicated genes, was carried out on the same mRNA samples that were used in two of the biological replicates in the microarray experiments. Two biological replicates were executed. The fold change in mRNA levels caused by (A) NFBD1 shRNA, (B) p53 shRNA, or (C) IR as determined by microarray and real-time PCR analysis is shown. 89% of the genes tested were regulated in the same direction according to both the microarray and real time PCR experiments.

Percent validation: 89%