## 4 Discussion
### Relation of KEGG and GO-Term Functional Analyses  
We used Gene Ontology term analysis as a parallel approach to KEGG, aiming to categorize DEPs through a different grouping framework and compare both outcomes. Many pathways categorized under biological process, such as thiamin metabolism, photosynthesis, nitrogen-containing metabolites processing, and cell death were also reflected in the KEGG analysis (Figure 4; Table 2). Similarly, spatial connections of cellular processes occurring in the chloroplast, stromule, mitochondrion, and glycosylome process, are related to several biochemical reactions described by KEGG pathways, since these take place in the relevant cell organelles. Both approaches for functional categorization seemed to be in line, suggesting specific pathways to focus on for future in-depth study regarding _C. pepo_ early spatiotemporal responses to _P. xanthii_ infection and RS elicitation. Highly Expressed Proteins in P. xanthii-Infected and RS-Treated Plants and Other Defense-Related Proteins of Interest  
Of the 297 proteins with an expression of above 2-fold (Figure 3B), 44 had an expression level ranging from 4- to 15-fold. Of these, 28 proteins were unique in treated plants (PX, RS, and RSPX) compared to Control (13, 7, and 8 DEPs, respectively), with the rest being shared among different groups (Figure 3C). Several of these 44 highly expressed proteins (Supplementary Table S1) including a starch branching enzyme, a thiamin thiazol synthase, ATPase subunit proteins, carboxylases, carbonic anhydrases, and kinases, were reported as members in different enriched KEGG pathways, and their putative functional roles through those biochemical pathways of various treatment cases have been discussed previously. Among the unique DEPs reported in the three treatments, which furthermore do not fall in a previously-reported KEGG pathway, two ABC-1 domain transporter proteins also annotated with a kinase activity, a glutaredoxin, and a lipid transfer protein in PX-related group, a tollB-related protein, an alcohol dehydrogenase, and a phosphoenolpyruvate carboxylase protein in the RS-induced group, and four proteins in the RSPX-related group,an ascorbate peroxidase, a 14-3-3 protein, a GDSL-lipase, and a protein of unknown function, are of further interest (Supplementary Table S1). In PX- and RS-treated samples, several defense-related proteins were among the significant DEPs, albeit with relatively low expression levels. These included a pathogenesis-related thaumatin-like protein (Cp4.1 LG20g08560.1), a pathogenesis-related protein PR-4 (Cp4.1 LG11g09910.1), and two leucine-rich repeat (LRR) family proteins (Cp4.1 LG15g04840.1; Cp4.1 LG01g02450.1). These proteins have been reported to play crucial roles in plant responses to pathogens [107; 108]. Although their roles are essential, the relatively low-fold changes in expression observed in different comparisons may be due to spatiotemporal influences, which will be discussed further. Among the 2070 annotated proteins, 70 were categorized under the term \"kinase\", with 28 of these being significant DEPs in at least one treatment group comparison (Supplementary Table S1). These include, among others, an ATP-dependent 6-phosphofructokinase (Cp4.1 LG01g09130.1), a pantotheane kinase (Cp4.1 LG09g10200.1), two previously reported ABC-1 domain-containing proteins (Cp4.1 LG05g14000.1; Cp4.1 LG11g05640.1), a mitogen-activated protein kinase (Cp4.1 LG13g01390.1), and an FGGY carbohydrate kinase (Cp4.1 LG07g08350.1) with fold expression levels ranging from 2- up to 6-fold in certain comparisons. Kinases belonging to these family types have been reported to play important roles in plant defense and hormone signaling [108; 109; 110; 111; 112; 113; 114]. It is worth noting that among the 70 reported kinases there is a receptor-like kinase 1 (Cp4.1 LG20g01680.1), a receptor lectin kinase (Cp4.1 LG15g03810.1), and a leucine-rich repeat protein kinase family protein (Cp4.1 LG03g0340.1).