Gene expression patterns in darkness and in response to light are affected in etiolated <i>hub1-3</i> mutant seedlings.

<p>(A) Genes misregulated in etiolated <i>hub1-3</i> as compared to wild-type (at the dark time point) were compared with light-regulated gene sets defined in wild-type seedlings at 1 h or 6 h. For relevant comparisons, the percentage of genes for which the <i>hub1-3</i> mutation mimics the effect of light on gene expression in darkness is given in red. (B) Clustering of gene expression data by Self Organizing Mapping (SOM). In each partition, the pattern reflects a general trend of expression gradient between 1 and 6 h of light for wild-type and <i>hub1-3</i> seedlings. The four points in each partition represent the experimental conditions of the four microarrays (<i>hub1-3</i>/wild-type in dark not included in this analysis) and the vertical bars at each point show variance in the group. All genes are assigned to just a single class. (C) RT-qPCR validation of selected upregulated genes in SOM class 1 (<i>left panels</i>) or downregulated genes in SOM class 4 (<i>right panel</i>) during de-etiolation in wild-type and <i>hub1-3</i> seedlings. RNA levels are given as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002825#pgen-1002825-g003" target="_blank">Figure 3A</a>.