- Course overview
- Search within this course
- Why do we need a pathway database?
- What is Reactome?
- When to use Reactome
- Who is Reactome for?
- Navigating Reactome
- Analysing data
- Programmatic access
- Contributing to Reactome
- Summary
- Try it yourself!
- Your feedback
- Get help and support on Reactome
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Diagram panel features
There are a range of tools in the diagram panel to help users to easily and effectively use this interface as pointed out in Figure 17. Some additional features are explained here.
External interactors
External interactors are not inherently a part of Reactome but rather they are proteins and small molecules that are reported to interact with entities in Reactome. Importing these interactors extends the content of Reactome. The default source for external interactors is IntAct database and users can customize this using the settings panel (icon 8 in Figure 17).
Interactors from IntAct are overlaid on Reactome data and shown as numbered red balls on the top right corner of corresponding entities in SBGN diagrams (Figure 25). Numbers represent the different interactors present for the entity. Clicking on this red ball pops out the associated interactors with a slider to adjust the confidence of the interaction. To get more details of the interaction, users can click on the edge connecting the interactor with the entity. This opens an IntAct tab with elaborate information on the interaction evidence.
Information panel
Within the SBGN diagram, hovering the mouse pointer or right-clicking on the glyphs representing a molecule, complex or reaction presents you with an information panel (Figure 26) that has three tabs:
- Molecules: Lists the component molecules for a complex or set
- Pathways: Displays a list of all other pathways that include the selected item as a participant
- Interactions: Shows a list of the molecular interactors from an external source (IntAct by default)
Colour customisation
The settings panel is a hidden slider, located on the right side of the diagram panel (icon 8 in Figure 17) and can be revealed by clicking. It can be used for context-sensitive help, to configure colour schemes and the source of interactors (Figure 27).
Illustration/Thumbnail
The illustration thumbnail is the rectangular compartment in the bottom left corner of the diagram panel (icon 10 in Figure 17). This feature allows you to focus on specific areas of the diagram via click and drag. Occasionally, a pathway diagram may have an additional thumbnail with the SBGN-complement figure (Figure 28). This helps users to switch between the SBGN and the complementary view to effectively understand the interactions.
