Figure 6.

Expression profiles classified by hierarchical cluster analysis. The y axis represents log₁₀ ratios of the signal intensities of corresponding probes of GA-treated and untreated seeds of plants indicated on the x axis, namely the wild type (WT), gid1, slr1, gid2, and gamyb. Threefold differences in intensity (±0.48 differences in log₁₀ ratio) are indicated as dashed lines. Purple lines represent the expression profiles of two representative genes for each group, which were confirmed by qRT-PCR (Supplemental Figs. S4–S7). The expression profiles of RAmy genes are shown as light blue lines in A, those of RAmy1A, RAmy1B, RAmy1C, RAmy3B, RAmy3C, RAmy3E, and RAmy3D are shown in C, and those of RAmy3A are shown in G. Green lines in C and H represent the expression profiles of genes having obvious downward outliers in gid2 and/or gamyb, which were confirmed by qRT-PCR (Supplemental Figs. S5 and S7). The arrowhead in B shows the obvious downward outlier Os04g0364800, which was confirmed by qRT-PCR (Supplemental Fig. S4D). The arrow in D shows Os11g0138300, an obvious downward outlier that was confirmed by qRT-PCR as presented in Figure 5B (probe 120).