2.4.3. Functional Enrichment Analysis of Genes in Interested Modules

We performed pathway enrichment analysis on the genes of each module separately, explored their related functions, and obtained many meaningful KEGG pathway and GO terms (Figure 10). It is important to identify the most significant modules related to medicinal components. Sienna3 module showed a significantly high correlation with polysaccharide. In the KEGG pathway, it is significantly enriched to fructose and mannose metabolism (ko00051), starch and sucrose metabolism (ko00500), and galactose metabolism (ko00052). The top three GO terms, shown in expanded size, are glucosyltransferase activity (GO:0046527) and starch synthase activity (GO:0009011). These KEGG pathways and GO terms are all related to polysaccharide biosynthesis, and polysaccharides are the main medicinal components of *Dendrobium*.

In addition, the KEGG pathways regulating *Dendrobium* polysaccharides and secondary metabolism biosynthesis were also identified in three other modules, which are the blue module, the lightsteelblue1 module, and the salmon4 module (Figure 11). In blue module, genes were significantly enriched in these pathways: anthocyanin biosynthesis (ko00942), drug metabolism—cytochrome P450 (ko00982) and steroid biosynthesis (ko00100). In lightsteelblue1, the significantly enriched pathways are as follows: terpenoid backbone biosynthesis (ko00900), diterpenoid biosynthesis (ko00904), galactose metabolism (ko00052), and glycolysis/gluconeogenesis (ko00010). In salmon4, genes were significantly enriched in these pathways: the pentose phosphate pathway (ko00030), terpenoid backbone biosynthesis (ko00900), and diterpenoid biosynthesis (ko00904). The enriched pathways in these three modules are significantly related to the synthesis of polysaccharides and secondary metabolites of *Dendrobium*. Therefore, sienna3, blue, lightsteelblue1 and salmon4 modules were defined as important module and extracted for further analysis.

**Figure 10.** GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of module sienna3. (**a**) Top 30 of KEGG pathway enrichment. (**b**) Thumbnails view of directed acyclic graph (DAG) on molecular function of module sienna3.

**Figure 11.** Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of interested module. (**a**) Module blue; (**b**) module lightsteelblue1; (**c**) module salmon4.
