## 3 Results
### Functional Enrichment Analyses of C. pepo Differentially Expressed Proteins
#### 3.2.2 GO-Term Analysis
Enriched pathways which are common or unique in the three comparisons between the treated sample groups (PX, RS and RSPX) and the Control, and in the three comparisons between the treated sample groups are presented in the upper and lower part of the table respectively. The numbers of differentially expressed proteins and corresponding _p_-values are presented under each comparison for each pathway. Figure 4: Gene Ontology terms (GO-terms) functional enrichment analysis of DEPs for all six comparisons (**A**–**F**) between the four treatment sample groups. Treatment names are as described in Table 1. GO-terms are presented as bar-plots on the left side of the figure, and using g:Profiler-type table outputs on the right side of the figure, respectively. The bar-plot panels on the left present quantitative data (counts) regarding up- and down-regulated DEPs, categorized from top to bottom according to significance (smaller to higher adjusted \(p\)-values), and irrespective classification of DEPs in main functional categories. The table panels on the right present the same GO-terms further categorized into three functional groups: biological process (BP), cellular component (CC), and molecular function (MF). GO-term IDs and sizes are also presented along with \(p\)-value significance scores. Functional analysis regarding the Biological Process category revealed that 16 GO-terms were enriched, with thiamin (GO:0009228), and oxazole and thiazole (GO:0018131) biosynthetic processes enriched in positive or negative regulation in four different comparisons and positioned high up regarding significance (Figure 4A,C,D,F). Other terms included photosynthesis-related processes (GO:0010207) found in PX vs. Control (Figure 4A); ion homeostasis and transport (GO:0070838; GO:0030003), oxidation and reduction (GO:0042744; GO:0055114), and cell death (GO:0008219) all reported in the RS vs. Control comparison only (Figure 4B); cyanide and nitrile metabolic processes (GO:0019500; GO:0050898), detoxification of nitrogen compounds (GO: 0051410), and cellular response to DNA damage stimulus (GO:0006974) found enriched in the RS vs. PX and RSPX vs. RS comparisons (Figure 4D,F). In the Cellular Component category, there were seven GO-terms that were significantly enriched. These were associated with the chloroplast (GO:0009941; GO:0009535; GO:0009507; GO:0009569), with the first two spanning all three different comparisons of treated samples (PX, RS, and RSPX) versus Control (Figure 4A-C); stromule (GO:0010319), found enriched in RS vs. PX and RSPX vs. RS comparisons (Figure 4D,F), fatty acid-breakdown-related glycosylome (GO:0009514), and mitochondrion (GO:0005739) reported in PX vs. Control and RS vs. Control comparisons, respectively (Figure 4A,B). In the Molecular Function category, six (6) GO-terms were found to be significantly enriched. These terms were associated with cyanoalanine nitrilase and hydrolase activities (GO: 0047427; GO:0047558), zink ion binding (GO:0008270), oxidation and reduction functions (GO:0016491), and carbote dehydatase activity (GO:0004089), all reported in the RS vs. PX comparison (Figure 4D) with the first two also reported in RSPX vs. RS (Figure 4F). One term related to ribosomal constituents (GO:0003735) was reported in the RS vs. Control (Figure 4B).