## 3 Results
### Functional Enrichment Analyses of C. pepo Differentially Expressed Proteins  
#### 3.2.1 KEGG Analysis  
The KEGG analysis revealed pathways that were enriched either in common between different sample group comparisons, or uniquely for a certain comparison. A collective presentation of 26 enriched pathways deduced from all comparisons with \(p\)-values < 0.05 is shown in Table 2. The complete list of enriched pathways, including those with \(p\)-values ranging from 0.05 to 0.1, along with the specific gene IDs within each pathway, is provided in Supplementary Table S2.  
In the PX vs. Control comparison, four (4) pathways appeared unique; \"Pentose phosphate pathway; cepep00030\", \"Carbon fixation in photosynthetic organisms; cepep00710\", \"Proteasome; cepep03050\", and \"Fatty acid degradation; cepep00071\". The first two contained DEPs with expression differences greater than 4-fold. Similarly, four (4) pathways were exclusively enriched in the RS vs. Control comparison, the \"Biosynthesis of secondary metabolites; cepep01110\", \"Flavonoid biosynthesis; cepep00941\", \"Starch and sucrose metabolism; cepep00500\", and \"Tryptophan metabolism; cepep00380\", with the first one being the most enriched, featuring 25 proteins and highly differentially expressed DEPs across three of the four groups. In the RSPX vs. Control comparison five (5) unique pathways were reported; \"Pyruvate metabolism; cepep00620\", \"Fatty acid biosynthesis; cepep00061\", \"ABC transporters; cepep02010\", Biosynthesis of cofactors; cepep01240\", and \"Monobactam biosynthesis; cepep00261\". Five more enriched pathways the \"Glutathione metabolism; cepep00480\", \"Ascorbate and Aldarate metabolism; cepep00053\", \"Thianine metabolism; cepep00730\", \"Glyoxylate and dicarboxylate metabolism; cepep00630\", and \"Ribosome; cepep03010\" were also reported, with the first three being common in the PX and RSPX vs. Control comparisons, and the remaining two being common in the PX and RS sample groups vs. the Control.  
Three pathways were reported in all three comparisons of treated sample groups (PX, RS, and RSPX) with the Control, with \"Metabolic pathways\" being highly enriched with 47, 46, and 40 proteins annotated in the three comparisons, respectively.  
A smaller number of KEGG pathways were enriched in comparisons between the treated groups (PX, RS, and RSPX) (Table 2). In the RS vs. PX comparison, three pathways were enriched, including two previously-identified (\"Metabolic pathways\" (cep01100) and \"Biosynthesis of cofactors\" (cep01240)). In the RSPX vs. PX comparison, three enriched pathways were identified: \"Biosynthesis of amino acids\" (cep01230), \"Polychomb repressive complex\" (cep03083), and the previously-reported \"Carbon fixation in photosynthetic organisms\" (cep00710). Notably, \"Thianine metabolism\" (cep00730), previously reported in PX and RSPX vs. Control comparisons, was also enriched in the RS vs. PX and RSPX vs. RS comparisons, with a highly significant \(p\)-value (p.DE close to 0). Of the eight enriched pathways across comparisons, six contained DEPs with expression differences greater than 4-fold. Notably, in the RS vs. PX comparison, the \"Metabolic pathways\" contained almost all DEPs with highly significant differential expression.  
Figure 3: Venn diagrams showing the overlap and differences of DEPs with \(p\)-values < 0.05 shared between the three comparisons of treated (PX, RS, RSPX) samples versus the Control. Treatment names are as described in Table 1. Overlaps for expression magnitudes above 1-fold (**A**), 2-fold (**B**), and 4-fold (**C**) difference in expression are shown.