Figure 8.

Functional enrichment analysis of stress- and stimuli-related differential gene expression in reil1-1 reil2-1 at standard cultivation temperature compared with cold-acclimating Col-0 and reil1-1 reil2-1 at 1 d (1d), 1 week (1w), or 3 weeks (3w) after the shift to 10°C. Differential gene expression was determined relative to nonacclimated Col-0 at standard cultivation temperature. Z-scores, P values, and mean log₂ fold changes (log₂-FCs) of genes belonging to 1,940 GO terms were calculated (Du et al., 2010; Supplemental Table S4). A, Heat map of mean log₂-FC of the top 10 significantly enriched 135 GO terms that represented responses to stimuli or abiotic and biotic stresses. Ranking was according to top positive or negative z-score values with mean log₂-FC > +0.1 or < −0.1. GO terms are listed with ontology, description, and number of constituting genes. Boldface in the GO description indicates shared enrichment of the nonacclimated mutant (0 d) with the acclimating Col-0 at 1 d, 1 week, or 3 weeks. Two general stimuli- and stress-response GOs as well as the temperature, cold, heat response, water, drought, and osmotic stress-related GOs were added for comparison. All top-scoring GO terms were biological processes (P). B, Mean log₂-FC of GO terms from the nonacclimated mutant (0 d) and acclimating Col-0 at 1 d, 1 week, and 3 weeks (from left to right). All 135 acclimation- and response-related GO terms were included. The inset data show the Pearson’s correlation coefficient (r²) and the slope of a linear regression (s). The arrows indicate GO:0009631, cold acclimation.