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- 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!
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Understanding the Pathway Browser
The Pathway Browser is used to navigate and view the Pathway Overview and Pathway Diagrams. To launch it, click on the ‘Pathway Browser’ button (Figure 16) on the homepage.
The Pathway Browser has three main panels – hierarchy, diagram and detail. These three panels are interactively connected. Clicking on a pathway or reaction name in the hierarchy panel causes it to be highlighted, opens the corresponding pathway diagram in the diagram panel and populates the details panel. An overview of all the features in the Pathway Browser is shown in Figure 17.
The main features of the Pathway Browser are listed below:
- Menu bar: contains the following buttons
1. Home (top left): returns to the homepage
2. Species (top left): displays pathways inferred for selected organism
3. Citation: provides the current Reactome literature reference to cite
4. Analyze data: opens pop out window for data analysis
5. Video tour: gives a quick tour of Reactome’s key features
- Diagram Panel: contains various graphical illustrations of reactions and pathways at different levels of granularity
6. Layout: show/hide the three main panels of the pathway browser
7. Key: describes the shapes and symbols used in the diagram panel
8.Settings: displays options to choose colour profiles and interactors for diagram panel
9.Zoom/Move: allows zoom in and out and navigate diagram panel
10. Thumbnail: displays the selected region of pathway diagram
11. Search Diagram: allows text search for the current pathway diagram
12. Fit to Page: resizes the pathway diagram to fit the screen
13. Pathway Overview: returns to the pathway overview page
14. Voronoi Pathway Overview: opens an overview of pathways in a new tab represented as a voronoi map
15. Illustration: shows text-book style figures of pathway diagram (if available)
16. Export: allows to download a screenshot of the current diagram panel in PNG, SVG or pptx format
- Hierarchy Panel: contains a hierarchically organised list of the events, i.e. pathways and reactions, within Reactome
- Details Panel: contains supportive and supplementary details of reactions and pathways
Clicking on pathways and reactions in either the hierarchy or the diagram panel will take you to the corresponding page in the browser – with the appropriate hierarchy level, reaction diagram and details.