Figure 3

Transcriptomic analysis of pi4kß1ß2 roots. (a) Similarity between the pi4kß1ß2 roots transcriptome (compared to WT) and the stress-, hormone- or temperature- responsive transcriptomes. The 200 genes most up-regulated in pi4kß1ß2 roots compared to the WT and the 200 genes most down-regulated in pi4kß1ß2 roots compared to the WT were used as a signature to search for transcriptome experiments with the highest similarity. The similarity search was performed against the 56 root experiments classified as “stress”, “temperature” or “hormone” by Genevestigator (Hruz et al., 2008). Experiments were sorted according to Euclidean distance. Expression of the signature genes in the 10 most similar experiments are shown in color-scale; (b,c) Hierarchical clustering of curated root experiments dealing with the response to auxins. The 9 curated root experiments dealing with auxins in Genevestigator were retrieved. According to the expression in these experiments of the 200 most down-regulated (b) genes in our pi4kß1ß2 vs. WT root comparison, the genes and experiments were clustered with the Biclustering tool in Genvestigator. The same was done using the 200 most up-regulated (c) genes in our pi4kß1ß2 vs. WT root comparison. Similarities between expression profiles were determined using Pearson correlation. For each experiment, the duration of hormone treatment is indicated. Separated gene clusters with highest levels of induction/repression are labeled and genes are specified on the right panel; (d) Response of selected genes to auxin. Five-day-old seedlings were transferred to a medium containing 10 nM IAA, and roots for RNA extraction were harvested after 24 h. The data are presented in means ± SE, n = 9, with a Tukey honestly significant difference (HSD) multiple mean comparison post hoc test. Different letters indicate a significant difference (one-way ANOVA, Tukey HSD, p-value < 0.05).