Switch between workflow pages. Each major visualization has its own page.
Regulation_info, Gene_info, and Operon_info are loaded from the server automatically. Upload Data_input to create an Excel-readable Master_regulation_database.csv file. Optionally, you can override the three server reference files below.
Column A = Gene_UID of each Gene
Column B = FC = fold-change
Column C = pval = p-values
A preview of the generated database will appear here.
These tables are generated automatically after Step 1 finishes. They use the master database rows as input to the Pyodide blits GSEA runtime.
Server-parity Plotly figure rendered from enrichment and master rows.
Server-parity Plotly figure rendered from enrichment and master rows.
Server-parity Plotly figure rendered from enrichment and master rows.
Server-parity Plotly figure rendered from enrichment and master rows.
Server-parity Plotly figure rendered from enrichment and master rows.
This canvas shows the original regulation cascade without the Data_input FC and p-value information. Nodes are colored neutrally, while regulation arrows still use the regulation modus where possible. Use this sheet first to inspect the cascade structure before viewing the FC-colored network below. Mouse wheel zooms; drag to pan. Click nodes to highlight direct connections.
Build a directed network from columns A and B of the Master_regulation_database where arrows point from Regulator to Gene. Level 0 is placed on the outer ring, higher levels are drawn inward, and nodes are arranged around each circle to make edges from the main regulators as short as possible for the genes they regulate. Self-regulation is shown with curved self-arrows, and reciprocal-only relationships do not force nodes inward. Level 0 anchors are distributed across the full outer circle while preserving an order that shortens regulator-to-target edges where possible. Genes from the same operon count as one level 0 anchor and are kept lined up radially in operon order, with the first gene on the level 0 circle. Regulators and genes on level 1 and higher are also positioned around their level circles to stay close to the majority of their lower-level targets. Mouse wheel zooms; drag to pan. Click nodes to highlight direct connections. Node color is based on FC: positive values are green and negative values are red. Values with absolute FC below the FC threshold are light grey, and values with pval above the p-value threshold are also light grey. Use the FC threshold slider to adjust the FC cutoff and the logarithmic p-value threshold slider to adjust the p-value cutoff.
Step 3 uses the Master_regulation_database created in Step 1 above. First create the database, then click Visualize generated database.
This step dissects the Step 3 regulation map into isolated Level 1 units. A Level 1 unit is a connected component containing level 0 and/or level 1 nodes, with at least one level 1 node and no direct or indirect connection to level 2 or higher nodes. The first canvas shows all unregulated genes from the Master Regulation Database as FC-colored nodes, with genes from the same operon placed next to each other as touching node clusters. The second canvas shows the Level 1 units as comparable mini circular maps with all gene and regulator names displayed. The third canvas redraws the original Step 3 FC-colored network after removing only nodes from those Level 1 units; level 2 and higher nodes remain intact.
This final visualization uses the created Master_regulation_database to make a new Regulators Only Database. Only columns A, B, and C are used: Gene name, Regulator, and Modus. Rows without a regulator are removed, and rows whose Gene name is not also present as a Regulator elsewhere are removed. The resulting map therefore shows only regulatory interactions between actual regulators. In this final view, the regulators are arranged in a hierarchical horizontal layout instead of circular rings: level 0 regulators are placed with equal spacing on a broad lower smiley-shaped arc, with the middle regulators lowest, and higher regulatory levels are stacked upward.
Use this to check that comma, semicolon, tab, quoted fields, and unregulated genes are handled correctly.