## 3 Results
### Functional Enrichment Analyses of C. pepo Differentially Expressed Proteins
#### 3.2.2 GO-Term Analysis  
Gene Ontology term (GO-term) analysis was performed to relate potential biological functions--categorized into three groups; biological process (BP), cellular component (CC), and molecular function (MF)--to DEPs. A collective presentation of enriched GO-terms regarding all comparisons is shown in Figure 4. \begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline  & & \multicolumn{2}{c}{**KEGG Pathways**} & \multicolumn{2}{c}{**PX vs. Control 1**} & \multicolumn{2}{c}{**RS vs. Control**} & \multicolumn{2}{c}{**RSPX vs. Control**} \\ \hline
**Group 2** & **Map Code** & **Pathway Description** & **N 3** & **DEPs 4** & **p.DE 5** & **DEPs** & **p.DE** & **DEPs** & **p.DE** \\ \hline  & crep00030 & Pentose phosphate pathway & 85 & **4 6** & 0.021 & & & & \\  & crep00710 & Carbon fixation in photosynthetic organisms & 114 & **5** & 0.013 & & & & \\  & crep03050 & Proteasome & 90 & 5 & 0.005 & & & & \\  & crep00071 & Fatty acid degradation & 66 & 3 & 0.048 & & & & \\ \hline  & & Biosynthesis of secondary & & & & **25** & 0.021 & & \\  & & metabolites & 1593 & & & **2** & 0.042 & & \\
2 & crep00941 & Flavoud biosynthesis & 31 & & & **2** & 0.042 & & \\  & crep00500 & Starch and sucrose metabolism & 186 & & & **5** & 0.047 & & \\  & crep00380 & Tyrtopphan metabolism & 67 & & & 3 & 0.034 & & \\ \hline  & & crep00061 & Fatty acid biosynthesis & 62 & & & & 3 & 0.020 \\  & crep02010 & ABC transporters & 70 & & & & 3 & 0.028 \\
3 & crep01240 & Biosynthesis of cofactors & 311 & & & & 8 & 0.008 \\  & crep00620 & Pyruvate metabolism & 131 & & & & **4** & 0.035 \\  & crep00261 & Monobactam biosynthesis & 12 & & & & 2 & 0.005 \\ \hline  & & crep00480 & Glutathione metabolism & 113 & 5 & 0.013 & & 4 & 0.021 \\  & crep00053 & Ascorbate and adarate metabolism & 81 & 4 & 0.013 & & 4 & 0.007 \\  & crep00730 & Thiamine metabolism & 29 & 2 & 0.050 & & & 2 & 0.030 \\ \hline  & & Glycosylate and dicarboxylate & & & & & & & \\
5 & crep00630 & metabolism & 109 & **4** & 0.005 & 5 & 0.003 & & \\  & crep01200 & Carbon metabolism & 367 & 10 & 0.008 & **8** & 0.040 & & \\  & crep03010 & Ribosome & 475 & **13** & 0.042 & 10 & 0.028 & & \\ \hline  & & crep01100 & Metabolic pathways & 3036 & **47** & 0.021 & **46** & 0.000 & **40** & 0.003 \\
6 & crep00970 & Aminoacyl-tRNA biosynthesis & 74 & 4 & 0.009 & 3 & 0.044 & **4** & 0.004 \\  & crep00902 & Monoterpenoid biosynthesis & 2 & 1 & 0.022 & 1 & 0.021 & 1 & 0.018 \\ \hline  & & & **KEGG Pathways** & & & **RS vs. PX** & **RSPX vs. PX** & **RSPX vs. RS** \\ \hline
**Group** & **Map Code** & **Pathway Description** & **N** & **DEPs** & **p.DE** & **DEPs** & **p.DE** & **DEPs** & **p.DE** \\ \hline  & crep01240 & Biosynthesis of cofactors & 311 & **4** & 0.015 & & & & \\
7 & crep00910 & Nitrogen metabolism & 49 & 2 & 0.004 & & & & \\  & crep01100 & Metabolic pathways & 3036 & **10** & 0.042 & & & & \\ \hline  & & crep01230 & Biosynthesis of amino acids & 327 & & & **3** & 0.013 & & \\  & crep03083 & Polycomb repressive complex & 66 & & & **2** & 0.004 & & \\  & crep00710 & Carbon fixation in photosynthetic organisms & 114 & & & 2 & 0.014 & & \\ \hline
9 & crep00730 & Thiamine metabolism & 29 & **2** & 0.000 & & 2 & 0.000 \\ \hline  & & & & & & & & & \\ \end{tabular}  
* **1 PX:** _Podospharex xanthii_ inoculated; **RS:** _Reynourtia sachalinensis_ treated; **RSPX**: RS treated and subsequently PY inoculated. 2**Group:** groups of pathways that appear significantly enriched in certain sample comparisons. **3****N:** Number of proteins included in each pathway. 4**DEPs:** Differentially expressed proteins enriched in each pathway. 5**p.DE:** _p_-value < 0.05 for significantly enriched pathways. 6 Bold numbers show KEGG pathways that include DEPs with a difference in expression of > 4-fold.  
\end{table} 
Table 2: Functional enrichment analysis of differentially expressed proteins. Enriched KEGG pathways in all six comparisons between the four different sample groups (cases).