Figure 2

General overview of the filtered and normalised data for each of the time point comparisons. (A-D) The average of the replicated hybridisations for each time point is presented using MA-plots (samples are labelled with a Red dye and the reference with a Green dye). An increased noise at lower signal intensities is observed, as expected, as no absolute cut-off level for signal intensity is used in the data filtering process. However, genes at the low-intensity region are not identified as differentially expressed genes due to variation between the replicated hybridisations. (B) At 30 minutes the overall pattern is drastically changed, with several genes showing a >2-fold change in expression levels. (C-D) The same general pattern is observed for the data corresponding to 120- and 240-min treatments. An increasing number of differentially expressed genes are, however, observed. For (A-D) genes differentially expressed at one time point ● (30 min blue, 120 min red, 240 min green), two time points + (30 and 120 min red, 30 and 240 min blue, 120 and 240 min green) or three time points ▲ (purple) time points are listed in Additional data files 1 and 2 available online. Dashed lines indicate two-fold differential expression.