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Only those array features which were significantly 'increased' or 'decreased' in three out of three microarray comparisons were considered to have met our criteria for inclusion in the low stringency datasets.
All microarray comparisons were made with at least 3 animals in each condition, and only those genes having at least 2-fold difference and whose coefficient of variance was less than 100% were considered to be differentially expressed.
All microarray comparisons were performed in quadruplicates using dye swaps performed on the same RNA extraction (thus 4 arrays were used per sample class derived from two separate RNA extractions).
Microarray comparisons were also conducted with intact skin from challenged and control fish; these data were not reported due to relatively small expression changes.
Microarray comparisons were carried out between Pax3 GFP/+ and Pax3 GFP/PAX3-FKHR preparations from the hypaxial dermomyotome of somites at E9.5 and forelimb buds at E10.5.
The 5,715 genes that met our threshold criteria for at least one of the seven microarray comparisons were clustered using Short MinerSTEMes Expression Miner (STEM) [ 35].
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However, parallel proteomic and microarray comparisons are still extremely useful if a cell's response to a given stimuli or oncogenic conversion are to be properly deciphered.
Genes with the greatest difference in expression between females and males in the OA-control microarray comparisons are listed in Table 5.
The level of induction of the gene encoding the pyruvate decarboxylase PDC1 (At5g54960) was lower in the eH response, suggesting that the metabolic shift from aerobic to anaerobic fermentation associated with P. brassicae inoculation reported in the first microarray comparisons was also less pronounced in the partial resistant response than in the susceptible one.
Furthermore, because our microarray comparison was not to the whole brain, we were able to identify markers that are also expressed in other song nuclei and brain subdivisions in various combinations (Figure 2 and Table S4).
More strikingly, the slope of the regression line for the RNA-Seq comparison is 1.0, while that for the microarray comparison is 0.15, suggesting that the fold-changes measured by microarray for these genes are strongly compressed relative to the true fold-changes and helping to explain the observed discrepancies between the RNA-Seq and microarray data.
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