## 3 Results
### Identification of Cucurbita pepo Differentially Expressed Proteins
A Volcano-type graphical presentation of significant (\(p\)-value \(<\) 0.05) and non-significant (\(p\)-value \(>\) 0.05) DEPs, combined with log2 fold change (\(>\)1 and \(>\)2 criteria) in gene expression for all comparisons, is shown in Figure 2. This provides a visual overview of the proteins' expression magnitudes for the up- and down-regulated DEPs in all comparisons presented collectively in Table 1 and in detail in Supplementary Table S1. Moreover, DEPs having a difference in expression of 4-fold (absolute value) and above are shown with their corresponding IDs. A description of the DEPs state in each comparison follows, combining information from all three sources (Figure 2, Table 1, and Supplementary Table S1), and with a reference to indicative DEPs with high (\(>\)4-fold) expression. \begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Comparison** & **DEPs 1** & **DEPs** & **Up-Regulated 2** & **Down-Regulated 2** \\
**Case 1 vs. Case 2** & _p-Value \(<\) 0.05_ & \(>\)12-fold 1** & **in Case 1** & **in Case 1** \\ \hline PX vs. C 3 & 316 & 199 & 140 & 59 \\ RS vs. C & 438 & 163 & 126 & 37 \\ RSPX vs. C & 394 & 148 & 129 & 19 \\ RS vs. PX & 75 & 31 & 10 & 21 \\ RSPX vs. PX & 76 & 20 & 15 & 5 \\ RSPX vs. RS & 82 & 25 & 18 & 7 \\ \hline \hline \end{tabular} 1
[FOOTNOTE:1]Footnote 1: **DEPs**: Differentially Expressed Proteins; 2 DEPs \(>\) 12-fold 1 up- or down-regulated in Case 1, out of 2070 features; 3  
\end{table} 
Table 1: _C. pepo_ Differentially Expressed Proteins (DEPs) in bilateral comparisons of the four sample groups. Proteins numbers with a statistical significance threshold (\(p\)-value) \(<\) 0.05 are shown, further filtered with an absolute value of 2-fold change and above expression difference, and further categorized as up- and down-regulated in case. Figure 1: Heatmap of the top 100 Differentially Expressed Proteins (DEPs) in all _C. pepo_ phyllosphere samples. The horizontal coordinate (dendrogram) on the top represents the clustering of each sample replicate for each treatment. Treatment names are as described in Table 1. The vertical coordinate (dendrogram) on the left represents the clustering of DEPs along with protein CuGenDB IDs. The heatmap specifies the relative up- or down-regulation of DEPs according to the log2 Centered Intensity index at the bottom of the heatmap. For each individual heatmap box, the dark red and dark blue colors represent high and low expression, respectively. In the PX vs. Control comparison (Figure 2A; Table 1; Supplementary Table S1), of the 199 DEPs, 172 had a 2-to-4-fold change (increase or decrease) in their expression respectively, and the remaining 27 had a difference above 4-fold, with the highest at 12-fold. Highly up-regulated proteins included a starch branching enzyme (Cp4.1 LG03g01090.1), an acetylornithine deacetylase (Cp4.1 LG05g00150.1), v-type proton ATPase subunits A (Cp4.1 LG04g01070.1) and G (Cp4.1 LG08g11040.1), a putative carbonic anhydrase (Cp4.1 LG20g07260.1), a glutaredoxin (Cp4.1 LG11g06470.1), and a malate dehydrogenase (Cp4.1 LG11g091820.1). Highly down-regulated proteins included a lipid transfer protein (Cp4.1 LG01g16110.1), an acetyl-coenzyme A synthetase (Cp4.1 LG03g06490.1), and a proline-rich protein-like isoform X1 (Cp4.1 LG02g02430.1). In the RS vs. Control comparison (Figure 2B; Table 1; Supplementary Table S1) 126 DEPs were up-regulated after RS application, with 114 proteins having a 2-to-4-fold differential expression, and the remaining 12 a 4-fold and above increase in expression. Notably, two out of the 12 proteins, the previously-reported starch branching enzyme (Cp4.1 LG03g01090.1) and a plastid disulfide isomerase (Cp4.1 LG08g02890.1) had a 15-fold and nearly 8-fold increase, respectively. Five out of the 27 down-regulated proteins had an above 4-fold decrease in their expression, including a 60S ribosomal protein L7 (Cp4.1 LG03g14990.1) and a glycerate dehydrogenase (Cp4.1 LG15g05930.1), both with an 8-fold decrease.