The enrichment analysis performed using ClueGO identified molecular pathways that were overrepresented the most in the DEG lists. In leaves, 51 individual molecular pathways were enriched (Table S8), many of which were related to nucleosome assembly (e.g., DNA conformation change, DNA packaging), ROS metabolism and carbohydrate metabolism. In hypocotyls, 18 enriched terms were detected, several of which were related to the biosynthesis of fatty acids, cutin, suberin and wax, as well as phenylpropanoid metabolism (Table S8). In roots, only two pathways were significantly enriched (Table S8).
Additional analysis performed using the pathifier package highlighted 116 terms whose pathway deregulation scores (PDSs) had been significantly altered among organs or between treatments (Fig. 9). Deregulation was high among organs, with roots and hypocotyls having deregulation patterns opposite to those of leaves. Fewer terms were deregulated between treatments. In leaves, they included several pathways related to energy metabolism (e.g., citrate cycle), purine and pyrimidine metabolism and signaling (Fig. 9A). In hypocotyls, some of the most deregulated pathways were related to the metabolism of fatty acids (e.g., glycerolipid metabolism, glycerophospholipid metabolism, fatty acid elongation) and to ROS metabolism, which was represented by five ROS-wheel-related ontologies (Fig. 9B, Table S8). Other deregulated pathways were related to calcium metabolism and the biosynthesis of cutin, suberin and wax. In roots, stressed and control samples differed little in pathway deregulation.