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Table 4 Gene by gene concordance of relative expression levels between platform data and sample-matched QRT-PCR data

From: Comparison of the latest commercial short and long oligonucleotide microarray technologies

  QRT-PCR (avg. Ct) Affymetrix Agilent Amersham
GENE B J M B J M B J M B J M
CASP5 34.03 X 37.85 0 0 0.3 0 0 1 0.3 1 0
RAG2 X 26.36 X 0 1 0 1 1 1 1 1 1
TMPRSS5 30.82 31.70 36.19 1 0.7 0 0 1 1 1 1 0
WNT10B 28.33 28.20 27.32 1 1 1 0.8 0.8 1 0.7 0 1
MAPK4 25.07 29.70 26.83 1 0 0 0.3 1 1 0 1 1
CXCL10 24.58 35.37 32.26 1 0.3 0 1 _ _ 1 _ _
RPS6KB1 24.36 23.68 20.72 1 1 1 1 1 1 1 1 1
RME8 22.84 22.17 23.29 1 1 0 1 1 0.5 0 0.3 0
ALG8 22.64 21.75 22.40 0 1 0.7 0 0 0 0 0 0
THEM2 22.62 22.21 22.50 1 1 1 0 0 0 1 1 0.7
ERBB2 22.61 27.45 21.51 1 0.5 1 0.8 0.6 0.9 1 1 1
CCNB2 22.29 20.77 21.93 0 1 1 0 1 0.8 0 1 1
RAB17 22.27 34.69 23.78 1 1 1 1 1 1 1 _ 1
BCAS 22.27 21.27 20.60 0 1 1 0 0 1 0 1 1
Score 27.5 25.5 26
  1. The average Ct values (avg. Ct) for each of the 14 genes (the control gene ABL1 is not shown) were calculated from the Ct values obtained from all sample-matched QRT-PCR reactions per cell line (n = 3, BattP12 (B); Jurkat (J); MCF7 (M)). Lower Ct values indicate relatively higher expression levels (see supplemental Table 3 for all Ct values obtained for all 15 genes and for each RNA aliquot). We are reporting the fraction of replicate expression values, by gene and by cell line, from the array data that are over- (or under) expressed in agreement with -ΔΔCt QRT-PCR data (where a score of 1 indicates a perfect concordance). More precisely, the score corresponds to the number of "same direction" (over or under-expressed) expression ratios from array data and QRT-PCR data for a given gene obtained from a given cell line relative to the reference sample divided by the total number of ratios. Data points not detected by QRT-PCR were taken into consideration into the calculation (i.e. if the gene was not detected by QRT-PCR for a cell line the score corresponded to the number of times this data point was filtered by the platform). Dashes indicate filtered data points for all replicate arrays for a given cell line. Fractions in bold indicate the platform yielding the highest sum of the individual fractions for a given gene and a given cell line. Multiple platforms can yield the highest sum for a given gene. The sums of all values for a each platform are given in the last line of the table.