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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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- Get help and support on Reactome
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Pathway overview
The Pathway Overview is a graphical representation of all Reactome pathways in a hierarchical, space-filling graph. It provides an overview of all pathways that reflects Reactome’s hierarchical pathway structure. Reactome provides two different types of overview diagrams – network and voronoi view.
Network (Fireworks) view
The network or fireworks view is the default overview view of pathways in the Reactome website (Figure 20).
Key features:
- Pathways are represented as filled circles, known as nodes. The size of the node reflects the number of molecular entities (proteins, small molecules, genes, etc) within the pathway
- Lines, known as edges, represent connections between a pathway and its subpathways in the Reactome pathway hierarchy
- The uppermost level of the hierarchy is represented by a central node. These nodes are surrounded by a series of connected, concentric rings of nodes that represent sub-pathways, radiating outwards from the central node until the lowest hierarchical level is reached
The diagram is interactive and you can move around, zoom in and click on topics of interest to get more details.
Voronoi (Reacfoam) view
The voronoi or Reacfoam view needs to be activated by clicking the bubble icon next to the search tab in the diagram panel (icon 14 in Figure 17). This will open a new tab with pathways represented as proportionately packed cells (Figure 21). Each cell represents a Reactome pathway. The upper part of a cell shows the pathway name, the lower part contains the sub-pathways as embedded cells. The area covered by a cell is proportional to the number of proteins and small molecules annotated in the pathway and its sub-pathways. The primary advantage of the voronoi view over the network view is that voronoi cells make great use of the available screen space thereby dedicating more area for each pathway and sub-pathway. This property can be quite useful especially when trying to interpret analysis results of Reactome.
Textbook-style
Many pathways at the higher levels of the hierarchy are too large to be represented as a single, detailed reaction diagram. Instead they are represented as a graphically enriched textbook-style illustration (Figure 22) that represents the sub-pathways as clickable regions.
SBGN
Reactome follows the community standard Systems Biology Graphical Notation (SBGN) convention to represent reaction details. The SBGN format provides elaborate interactive information on reactions, adjacent reactions and participating molecules, among other details (Figure 23). Reactions associated with diseases are indicated with red boundaries and edges.
SBGN-complement
SBGN is the standard graphical representation of reactions in the community and is efficient in capturing various interaction information. However, this format is not very friendly to human eyes. To interpret reaction-level interactions better, Reactome provides easy to understand illustrations of the pathway (Figure 24). These simple figures are designed to complement the more complex SBGN diagram.
