## 2 Materials and Methods
### Step 6: Result Page Generation  
Upon completion of the analysis, the system provides the user with the results via a web-based interface, culminating in the presentation of the analysis results on a dedicated web page. This interface is illustrated in Figure 2. The results page consists of several informative elements, including an analysis results plot, a network visualization, and an analysis results table.  
The following paragraphs describe the contents of each tab in detail. The analysis results plots, starting with Figure 2A, provide a comprehensive overview of the results. The bar plot summarizes the results of the enrichment analysis on DEG with user-defined thresholds. This plot shows the top 10 functional enrichment results for GO categories, biological processes, cellular components, and molecular functions, as well as two biological pathways: WikiPathways and KEGG pathways.  
The volcano plot places significant DEGs by displaying the log2 fold change of a gene on the x-axis and the negative logarithm of the \(p\)-value on the y-axis. For ease of use, the top 20 most significant genes are labeled based on their \(p\)-value.Some labels may not be visible if they overlap on the plot, but the user can mouse-over to see the gene name. Network-level analysis plots visually represent significant DEGs associated with TFs at the network level. This plot shows the betweenness centrality score and the network propagation score (NPscore) on the axis, allowing users to identify significant genes within the network. A heat map showing gene expression patterns is the final plot. The heat map plot shows gene expression patterns.  
Figure 2: Analysis results of TFNetPropX. ((**A**) Analysis result plots.) A tab that displays the analysis result as an interactive plot. Even if there is no label, the tooltip for the entity will appear when the mouse is held over it. ((**B**) Network visualization.) A tab that visualizes the TF network results. Clicking on a node gives information about the gene and a link to the NCI gene search page. ((**C**) Analysis result tables.) This tab shows a table for each analysis result. These can be searched, sorted, and downloaded in CSV format. Clicking on each term provides a pathway DEG mapping plot or a link to the term.  
The second tab is the network visualization in Figure 2B, which allows the user to explore gene regulatory and interaction mechanisms. The result is a TF-TG visualization network connected by enriched functionally-related DEGs. In addition, by clicking on a node, the user can check the node-related information, log2 FC, NPscore, and centrality score, and it also provides a link to the NCBI gene search page.  
The third tab is the analysis result tables shown in Figure 2C, which allows the user to view the result in tabular form and download it by exporting it as a CSV file. Six tables are available to the user, including the DEG analysis results and five enrichment analysis result tables. It is also possible to search for a specific word in the column. Finally, clicking on a term in the table will take the user to the relevant link, so that they can immediately investigate the information associated with the term. The gene is linked to the NCBI link, the GO term to the AmiGO2 link, and WikiPathways to the WikiPathway website link. Finally, when the user clicks on a term in the KEGG pathway table, the user can check the biological function-related genes by displaying an image with DEGs mapped in red in the KEGG pathway image generated by KEGGAPI.