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Table 1 A comparison of average qRT-PCR, RMA, and MAS 5.0 scores and the corresponding correlation values for the 31 transcript-concordant genes assayed in this study for which the Affymetrix microarray probesets (Affy IDs) were deemed likely to recognize identical transcripts to qRT-PCR probes. Genes are ranked from lowest to highest average log2 RMA scores. Genes with significant correlations (p < 0.05) obtained by either normalization procedure are highlighted in bold. The number of specimens tested for each gene is included (n). Expression levels are shown as log2>.

From: Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR – how well do they correlate?

GENE   EXPRESSION CORRELATION
NAME AFFY ID n RMA MAS 5.0 qRT-PCR RMA-qRT-PCR MAS-qRT-PCR
LCE 204256_at 22 4.79 7.01 0.27 0.81 0.70
ALDH1A1 212224_at 22 4.93 6.66 -2.93 0.89 0.88
CFLAR 211317_s_at 13 5.61 7.92 -0.12 0.65 0.75
REL 206036_s_at 13 5.63 8.36 0.53 0.76 0.77
ABCC4 203196_at 22 5.84 7.54 0.09 0.78 0.89
FOXO1A 202724_s_at 19 5.91 7.43 -2.05 0.85 0.90
NOTCH2 212377_s_at 13 6.19 8.24 -0.43 0.77 0.82
TNFRSF21 214581_x_at 13 6.22 8.03 1.98 0.83 0.97
MADH9 206320_s_at 19 6.24 5.47 -2.29 0.87 0.74
PPM1D 204566_at 30 6.29 8.80 0.50 0.73 0.72
MAP7 202889_x_at 22 6.42 6.27 -3.51 0.85 0.87
DMBT1 208250_s_at 19 6.49 7.25 -6.49 0.20 -0.11
SNIP1 219409_at 13 6.57 8.34 1.08 0.69 0.77
OSF2 210809_s_at 19 6.59 7.68 -1.26 0.80 0.77
ATBF1 208033_s_at 19 6.64 7.14 0.27 0.81 0.84
KIT 205051_s_at 22 6.70 7.51 -2.73 0.86 0.87
P53 201746_at 19 7.00 8.50 -3.44 0.41 0.11
BAG3 217911_s_at 19 7.04 8.61 -0.98 0.79 0.82
RB 203132_at 19 7.04 9.14 -2.82 0.45 0.38
WBP4 203599_s_at 19 7.28 8.97 -0.24 0.62 0.74
BNIP2 209308_s_at 13 7.58 9.79 0.56 0.68 0.69
UMPCMPK 217870_s_at 13 8.17 10.98 1.10 0.37 0.12
DCAMKL1 205399_at 19 8.18 9.23 -3.57 0.76 0.89
OAZIN 201772_at 30 8.22 10.36 -0.36 0.72 0.77
LHFP 218656_s_at 19 8.37 9.27 -0.46 0.89 0.90
BTG3 205548_s_at 13 8.47 10.54 0.83 0.86 0.90
DCX 204850_s_at 19 8.81 10.08 0.62 0.87 0.88
TERF2 203611_at 19 9.05 10.04 -0.14 0.32 0.31
GADD45A 203725_at 19 9.17 9.80 -0.12 0.96 0.94
PRSS11 201185_at 19 9.22 9.85 -3.54 0.63 0.64
RAP1 201174_s_at 19 10.34 11.59 -0.82 0.83 0.84