The bzip1-1 mutation triggers different modes of de-regulation in response to N and L treatments (clusters 1 to 10). ANOVA identified 219 genes misregulated in bzip1-1 compared to a WT sibling that were then used for cluster analysis (see Methods). A heatmap is presented for each cluster, with the regulation of any single gene in it and the histogram is a centroid plot of the whole cluster expression. The whole cluster has been used in order to run a second ANOVA to detect the effect of the signals and the bzip1-1 mutation (Additional file 4). The results of the second ANOVA, together with the analysis of the centroid histograms, allowed us to build a conceptual model of the role of the bZIP1 gene for each cluster/mode of de-regulation. As in Boolean logic, a black circle drawn on an edge represents the negation of the signal (for example in cluster 17: "No light and no nitrogen induces cluster expression"). To simplify the interpretation of the figure, when the logic gate uncovered using the bzip1-1 mutant plants was different from the one derived for the WT-sib, the Boolean model has been colored in red (to right side of the Boolean conceptual models).