Figure 3

Vector analysis of gene expression responses in two genetic backgrounds in Arabidopsis plants. Each dot corresponds to a single sum vector from four pairwise comparisons (two replicates per background). Genes towards the periphery of the circle show the most consistent behavior among replicates. Two behavior prototypes are highlighted (corresponding to Gene 1 and 2 in Fig. 1), mutant-specific down-regulation (purple) and WT/Mutant-consistent up-regulation (orange). It can be seen that inconsistent genes (close to the center) are generally showing background-specific responses, i.e. they are enriched along the axes of the plot. Their behavior is most likely the result of spurious noise in a single replicate.