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This result indicated that there was good correlation between the microarray analysis and the qPCR analysis.

Pearson correlation coefficients between the microarray analysis and QRT PCR were calculated.

However, in most cases, there was good correlation between the microarray analysis and Q-PCR (Table 3).

This 94.1% (= 32/34 comparisons) agreement between the microarray analysis and the Q-PCR experiments is comparable or better than that observed in other microarray studies [ 39].

As shown in Figure 1, a strong correlation (Pearson's correlation 0.894) was found between the microarray analysis and the qRT-PCR results, which indicated a good concordance of both methods.

We found that SOX7 (p < 0.01) and SOX10 (p < 0.01) genes showed a significant down-regulation in tumor tissues and SOX9 (p < 0.01) gene showed a significant up-regulation in tumor tissues when compared to corresponding adjacent benign prostate tissues, although the fold change in the expression level was not exactly same between the microarray analysis and QRT-PCR.

Similar(54)

EEF1A1 was selected as a reference gene for normalization due to its low variation between samples in the microarray analysis.

Four genes showed more than two-fold differences between breeds in the microarray analysis, but were not statistically significant.

To assess the significant differences between groups in the microarray analysis, a >1.5 fold change filter and permutation based t-test (p <0.05) were performed using the TIGR Multi Experiment Viewer [ 49].

The western blot procedure was also run using the pre-immune serum for a comparison with the immune serum and all samples were analysed using a rabbit anti-β tubulin polyclonal antibody as a control since the corresponding gene was not significantly different between the ranks in the microarray analysis described above.

The genes selected for qRT-PCR validation differed significantly among strains (gad2 gfap pomca), between wild and domesticated strains (sepp1a synpr), or between the sexes (dio2) in the microarray analysis.

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