2.4. Construction of saponin biosynthesis regulatory network under MeJA treatment

Differentially expressed genes (DEGs) (TPM > 1 and coefficient of variation (CV) > 0.1) were used to generate a regulatory network for saponin biosynthesis under MeJA treatment using the weighted correlation network analysis (WGCNA) package. The parameters were determined based on the previously described method [54]. The initial modules were merged using eigengenes to identify the key modules regulating saponin biosynthesis. This package was then used to calculate eigengene values for each module, to establish the relationship between metabolites and the modules associated with saponin biosynthesis. The Muffuz package [55] was used to partition the selected module sets into different clusters based on expression similarity patterns to obtain the core genes responsible for regulating saponin biosynthesis under MeJA treatment.