Figure 2

Comparison of expression data between platforms. P450 expression data generated using a spotted microarray covering gene specific PCR products (CYP-array) were retrieved from the 'Functional Genomics of Arabidopsis P450s' web page (Table 1). In this analysis, signal intensities in roots from 1 week old seedlings were generated by comparison to a 'universal RNA' sample [2]. Not detectable intensities were artificially set to a ratio of 0.05 compared to the 'universal control' and after log₂-transformation expression data were mean centered across the experiments. Expression data from published Affymetrix ATH1 array hybridizations were processed as described in Methods. The mean intensities from 17 experiments derived from young roots were selected. To generate a control similar to the 'universal RNA', mean intensities from 69 experiments covering similar samples were calculated and log₂ ratios were generated. Shown is a 2 × 2 plot comparing the mean centered expression ratios [log₂(sample/mean)] from both platforms using data for all P450 genes represented on both array types. Data points following the same trend are shown in black, points which are more than twofold different from the average expression in one platform, but less than twofold different in the other are shown in gray. Red dots indicate genes with opposing expression using the two platforms