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.