## 2 Results
### Detection of Transcription Factor Families  
Transcription factor (TF) families participate in a wide variety of biological processes in plants and have important roles in regulating the activity of triterpen saponin biosynthesis and other secondary metabolic processes. A total of 4381 unigenes encoding TFs were identified in the C. chinese transcriptome database and classified into 59 different TF families, including 752 upregulated unigenes in the leaf versus root comparison and 561 upregulated unigenes in the stem versus root comparison (Table 4). We concluded that the MYB family (572 unigenes) accounted for the largest  
\begin{table}
\begin{tabular}{l l l l} \hline \hline \multirow{2}{*}{**Hormone**} & \multirow{2}{*}{**Number of Unigenes**} & \multicolumn{2}{c}{**Number of UPEgulated Genes**} \\ \cline{3-4}  & & **Leaf vs. Root** & **Stem vs. Root** \\ \hline JA & 60 & 8 & 24 \\ GA & 10 & 0 & 1 \\ ABA & 27 & 6 & 11 \\ Total number & 97 & 14 & 36 \\ \hline \hline \end{tabular}
\end{table}
Table 3: Classification and number of hormone identified in the DEGs database for C. chinese.  
Figure 7: Number of DEGs in the most enriched pathways. (**A**) Number of upregulated DEGs in stem vs. root and leaf vs. root samples involved in terpenoid and polyketide metabolism. (**B**) Number of upregulated DEGs in stem vs. root and leaf vs. root samples involved in the biosynthesis of other secondary metabolites.  
proportion of TF families, followed by MYB-related (433 unigenes), AP2-EREBP (345 unigenes), bHLH (282 unigenes), WRKY (277 unigenes), NAC (206 unigenes), GRAS (168 unigenes), and C3H (160 unigenes). Furthermore, we confirmed that the MYB (nine unigenes), MYB-related (nine unigenes), and FHA (five unigenes) TF families were involved in metabolism of terpenoids and polykeptides, and that 12 TF families participated in biosynthesis of other secondary metabolites (Figure 8).  
\begin{table}
\begin{tabular}{l l l l} \hline \hline \multirow{2}{*}{**TF Family**} & \multirow{2}{*}{**Number of Unigenes**} & \multicolumn{2}{c}{**Number of UPEGulated Genes**} \\ \cline{3-4}  & & **Leaf vs. Root** & **Stem vs. Root** \\ \hline MYB & 572 & 100 & 75 \\ MYB-related & 433 & 66 & 54 \\ AP2-EREBP & 345 & 19 & 21 \\ bHLH & 282 & 64 & 47 \\ WRKY & 277 & 76 & 29 \\ NAC & 206 & 32 & 13 \\ GRAS & 168 & 15 & 14 \\ C3H & 160 & 16 & 17 \\ G2-like & 132 & 30 & 17 \\ CZH2 & 102 & 18 & 9 \\ MADS & 102 & 31 & 29 \\ Trihelix & 92 & 16 & 17 \\ Tify & 89 & 21 & 11 \\ HSF & 86 & 12 & 8 \\ mTERF & 78 & 21 & 17 \\ C2C2-Dof & 76 & 14 & 2 \\ FAR1 & 71 & 14 & 10 \\ RWP-RK & 68 & 16 & 7 \\ C2C2-GATA & 64 & 9 & 6 \\ ABBVP1 & 62 & 4 & 11 \\ ARF & 61 & 0 & 14 \\ SBP & 60 & 7 & 21 \\ Alfin-like & 50 & 5 & 5 \\ TAZ & 49 & 14 & 11 \\ TUB & 47 & 0 & 2 \\ bZIP & 44 & 6 & 6 \\ LOB & 43 & 1 & 0 \\ TCP & 40 & 18 & 7 \\ LIM & 40 & 4 & 8 \\ FHA & 40 & 7 & 6 \\ other & 442 & 96 & 67 \\ Total number & 4381 & 752 & 561 \\ \hline \hline \end{tabular}
\end{table}
Table 4: Classification and number of TF families identified in the DEGs database of C. chinense.  
Figure 8: Transcription factor (TF) families in the metabolic pathway. (**A**) TF families in the metabolism of terpenoids and polykeptides. (**B**) TF families in the biosynthesis of other secondary metabolites.