Figure 2.

Profiles of genes differentially expressed (P < 0.05) in imbibed nitrate-treated seeds versus control seeds and their profiles in nitrate and seed transcriptomes. The different transcriptome experiments with imbibed nitrate-treated seeds versus control imbibed C10 seeds are indicated on the left as well as the log₂ ratios of gene expression in tested versus control conditions (first column). Red shading indicates overexpression, green shading indicates underexpression in tested versus control samples, and black shading indicates no differential expression. Profiles are compared with those in published array data (second to sixth columns): nitrate provision to starved plants (Scheible et al., 2004; NO3 versus starv); comparison of Ler seeds imbibed at 4°C and 22°C imbibed seeds (Yamauchi et al., 2004; stratif versus 22°C); nitrate-treated primary dormant Cvi seeds after-ripened for 91 d and then imbibed for 24 h in the light compared with the same seeds imbibed in the light without nitrate (Finch-Savage et al., 2007; PDLN versus PDL); cold-treated primary dormant Cvi seeds after-ripened for 117 d compared with 20°C imbibed primary dormant Cvi seeds in the dark (Finch-Savage et al., 2007; PDC versus PD24h); and after-ripened Ler seeds imbibed for 24 h compared with freshly harvested Ler seeds imbibed for 24 h (Carrera et al., 2007; Ler AR versus Ler D). In all cases, log₂ ratios of expression are indicated. Gray shading indicates genes absent on the Affymetrix chips. Gene identifiers and functions as well as the values of the log₂ ratios in the different experiments are provided in Supplemental Tables S1 to S3.