Pathway Overview

Network (fireworks) view: Each pathway in the network view of pathways is coloured in different shades of yellow according to the over-representation significance (p-value) (Figure 12). A selection bar at the bottom of the Diagram panel will allow you to colour pathways based on the coverage (number of matched entities) instead of p-value.

Voronoi (Reacfoam) view: The voronoi map can be generated by clicking on the bubble-themed icon on the top of the Diagram panel. This opens a new tab with the same information as in the network view but this view is easier for users to visualise the results (Figure 13).

Textbook-style diagrams represent analysis results within the label for subpathways. The label background changes from blue to white, a yellow band is used to indicate the proportion of the pathway that is represented in the query dataset. A grey bar above the label indicates the number of pathway entities that is represented in the query dataset, the total number of entities in the pathway, and the FDR corrected probability score (Figure 14).

SBGN diagram: Entities in the diagram are coloured yellow if they were represented in the submitted data set. Complexes, sets and sub-pathway icons are coloured to represent the proportion of the molecules they contain that are represented in the submitted identifier list. In Figure 15, PIK3R1 is yellow indicating that is was in the submitted list. The complex GRB2:GAB1:PIK3R1 is part yellow, indicating that some molecules in the complex (PIK3R1) were represented in the submitted dataset while others (GRB2 and GAB1) were not.