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The Pathway Browser is the primary means of viewing and interacting with pathways in Reactome. It includes tools for analysing datasets and exploring pathways. These tools allow several types of analysis:

  • Pathway over-representation analysis and pathway topology-based analysis
  • Comparison of a pathway with its equivalent in another species
  • The overlay of user-supplied expression data onto a pathway
  • The overlay of protein-protein or protein-compound interaction data from external databases or user-supplied data onto a pathway  

See the section Reactome Tools for details of the analysis tools.

The Pathway Browser is launched by clicking the Browse Pathways button on the Homepage:

pathway browser button

When the Pathway Browser opens, it displays an overview of all Reactome pathways. Pathways are organized hierarchically and often have sub-pathways. At the highest hierarchical level, all pathways are represented in an Overview. At intermediate levels, pathways are often represented as interactive illustrations, with selectable regions that act as links to the lower levels, which are represented as detailed Pathway Diagrams. Reactome’s Overview uses a unique graphical visualization of the hierarchy, representing pathways at the uppermost hierarchical level as central nodes (circles) with subpathways arranged concentrically (in rings) around them. Many have further concentric rings of ‘child’ subpathways. Pathway nodes are connected to their subpathways by edges (lines). This overview displays all pathways and allows rapid zooming to details. As you zoom in, labels appear for the subpathway nodes. This view is also used to display data analysis results.

Nodes in the overview link to detailed pathway diagrams that use a style based on Systems Biology Graphical Notation. They have several features intended to ensure an appropriate level of information detail, including subpathway shading and fade-in of labels, commonly occurring small molecules and structures.

To see the details of a specific pathway, select and click (or double-click) the node representing the pathway. Alternatively select and click on the name in the Pathway Hierarchy panel on the left.

Features of the Pathway Browser are labelled in the diagram below.  

pathway browser labelled

Home – the Reactome logo is a button linked to the homepage.

Species – Reactome is a database of curated human biological pathways. These human pathways are used to computationally infer equivalent pathways in model organisms (described in detail here). Use the Species drop-down to select a species and view the predicted pathway. Note that infectious disease pathways that show the interaction of pathogens with human proteins are included in Homo sapiens.

Layout – The pathway browser is divided into 3 main sections. These are: the Hierarchy Panel, on the left, the Details Panel, bottom right, the Pathway Panel, top right. The layout buttons allow you to show or hide these panels.

Analyse Data – Opens a panel where analysis can be performed.

Key – this opens a key explaining the objects present in the pathway panel.

Zoom/Move Toolbar - Click on the arrows to move the diagram. Click on the plus and minus buttons to zoom in and out. Alternatively, click and drag the diagram, and use your mouse scroll wheel to zoom.

Search Diagram – click the button to open the search panel. When the Overview is displayed, this search considers all of Reactome. When a Pathway Diagram is displayed, only objects represented in the displayed diagram are searched.

Fit to Page - resizes the Pathway Overview or Diagram to fit the available space.

Open Diagram – when a pathway node is selected in the Pathway Overview, this button opens the corresponding Pathway Diagram

Illustrations – some Reactome pathways have a corresponding high-quality graphic. Select this button to view.

Export – use this button to download the visible region of the Pathway Overview or Diagram, including any analysis overlay, as a PNG file or upload it to GenomeSpace.

Thumbnail – Provides an overview of the entire pathway when zoomed in so that only a region of the pathway is displayed.

Pathway Panel - This is where Pathway Diagrams are displayed when they are selected in the Pathway Hierarchy or in search results. If no pathway is selected, this panel displays a brief Reactome help guide.

Details Panel - Contains details of objects when they are selected in the Pathway Diagram. The content depends on the type of object, i.e. pathway, reaction, complex, set, protein or small molecule (see the Details section).

Hierarchy Panel – Includes the hierarchical organisation of Reactome pathways and pathway events or steps, known as reactions. When the Pathway Browser is opened, only the top level of the hierarchy is shown, as an alphabetical list of Reactome’s main topics. Most topics are too large to be represented as a single diagram. Instead they are split into sub-pathways, which may be further divided into sub-sub-pathways. Most topics in Reactome are organised in this hierarchical manner. Sub-pathways can be revealed by clicking on the + icon to the left of the pathway name, and hidden by clicking on the - icon.

Settings sidebar – Used for context-sensitive help, to configure colour schemes and the default source of interactors.

Pathway names are preceded by the icon  . As sub-pathways are revealed, at some point a level is reached where the reactions will become visible. Reactions names are preceded by the icon  . You may also see the icon   representing “black-box” reactions, where the full molecular details have been omitted for clarity, or the details are incompletely determined.

The order of reactions from top to bottom in the Hierarchy Panel usually follows their order as steps in the pathway so that the preceding reaction is above and the subsequent reaction below, but this is not always the case. Pathways may not be linear; they can be circular or branched. Consequently, reactions often have multiple preceding or subsequent reactions. These connected events are often visible within the pathway diagram but can be part of a different pathway diagram. To view a complete list of the events that precede or follow a reaction, refer to the Preceding and Following Events section in the Details Panel, as described in the Details Panel chapter below.

Pathway Diagrams

Pathway Diagrams represent pathways as a series of connected molecular events, known in Reactome as ‘reactions’, which can be considered as steps in the pathway.

Cellular compartments are represented as pink/orange boxes with a double boundary. A typical diagram has a box to represent the cytosol, bounded by a double-line that represents the plasma membrane. The white area outside this box represents the extracellular space. Other organelles are represented as additional labelled boxes within the cytosol.

Molecules, represented in diagrams as blue/green boxes, are placed in the physiologically-correct cellular compartment, or lie on the boundary of a compartment to indicate that they are in the corresponding membrane, e.g. a plasma membrane protein will be placed on the boundary of the cytosol.

Reactions typically include:

  • Input and output molecules, and when relevant a catalyst (see diagram A below)
  • Inputs, outputs and catalyst are represented as boxes or ovals
  • Green boxes with rounded corners are proteins
  • Green boxes with square corners are proteins that have no UniProt accession (or did not at the time the reaction was created).
  • Green ovals are small molecules or sets of small molecules
  • Blue boxes with a double boundary are sets, i.e. proteins or small molecules that are functionally equivalent.
  • Blue boxes with cut corners are complexes, i.e. proteins and/or other molecules that are bound in a multimolecular entity.
  • Green boxes with a white inner box are sub-pathways.
  • Reaction input and output molecules are joined by lines to a central ‘reaction node’ (surrounded by a green box in Figure A below). Clicking this node selects the reaction.
  • The outputs of a reaction have an arrowhead on the line connecting them to the reaction node.
  • Reaction inputs/output molecules are often connected by arrows to preceding or subsequent reactions (i.e. the preceding/subsequent steps in the pathway).
  • Catalysts are connected to the reaction node by a line ending in a circle.
  • Numbered boxes on the line between an input/output and the reaction node indicates the number of molecules of this type in the reaction (when n >1).
  • Molecules that regulate a reaction are connected to the reaction node by a line ending in an open triangle for positive regulation or a ‘T’-shaped head for negative regulation (see B below).
  • A white box labelled P on the boundary of an object indicates a phosphorylation event.
  • Proteins or small molecules that are also part of a displayed set may be connected to the set object by a line of short dashes.
  • Sets with overlapping content may be connected by a line of long dashes.
  • Reactions that represent a disease process use red connecting lines. Objects associated with a disease are bordered in red.

Enhanced high-level diagrams and Subpathway icons

Many pathways at the higher levels of the hierarchy are too large to represent as a single, detailed pathway diagram. Instead they are often represented as an illustration, known as an enhanced high-level diagram, which graphically represents the subpathways as selectable regions of an illustration. When the mouse pointer is moved over a region, it becomes surrounded by a blue highlighting 'halo'. When you click on a region it becomes selected and outlined in dark blue, the corresponding subpathway is selected in the Hierarchy panel and the Details panel updates to show details of the subpathway. Double-clicking on a region opens the corresponding detailed Pathway Diagram.

In the Hierarchy panel, pathways that have an enhanced high-level diagram have a blue icon to the left of their name.

EHLD

A few higher level pathways use an older visualization of large topics, where subpathways are represented by a box with a green boundary, the subpathway icon (see example below). Selecting a subpathway icon has the same result as selecting a region of an enhanced-level pathway diagram as described above.

green boxes

In diagrams of lower level pathways, Reactome links to other related pathways through green boxes. In order to differentiate between related subpathways that are children of the same parent pathway (subpathways) and related subpathways that are children of a different parent pathway (interacting pathways), the Pathway Browser uses slightly different glyphs as illustrated in the figure below.

subpathways interacting

Subpathway Shading

When a Pathway Diagram contains subpathways, the area containing each subpathway is overlaid with a coloured box, labelled with the subpathway name, to help locate it in the larger diagram. Below is the diagram for ERBB4 signaling. The four subpathways are represented as 4 boxed and shaded areas.

Pathway Diagram zoom detail level

The pathway diagram represents different levels of detail, depending on the zoom level. When fully zoomed-out, regions corresponding to subpathways are shaded. The boxes representing molecules or groups of molecules have no text labels and trivial molecules, such as water and ATP, are not represented. At the next level of zoom, subpathway shading disappears, while trivial molecules and the circular red icon indicating that a protein has known interactors fade into view. At closer levels of zoom the reaction nodes appear, as do boxes containing a number on the lines connecting molecules to the reaction node if stoichiometry is greater than one. At this level of zoom, if interactors are displayed their names appear. At the highest level of zoom, if available, proteins, small molecules and interactors display structural diagrams from PDBe or ChEBI with associated details.

Navigating Pathway Diagrams

The Pathway Diagram, Hierarchy and Details Panels are interactively connected. Selecting an entity (molecular object) or event in the diagram will reveal relevant information in the Details Panel. Clicking a pathway name in the Hierarchy will open the corresponding Pathway Diagram in the Pathway Diagram Panel, and reveal details of the pathway in the Details Panel. If a subpathway is contained within the diagram that is displayed, clicking its name in the hierarchy will cause all the reactions in the pathway to be highlighted in blue. In the figure below, the diagram for Platelet homeostasis is displayed in the Pathway Panel, and the sub-pathway Prostacyclin signalling through prostacyclin receptor has been selected in the Hierarchy, causing all the reactions in this sub-pathway to be highlighted (blue) on the Pathway Diagram.

subpathway selection

Similarly, selecting a reaction in the Hierarchy causes that reaction to be highlighted in the pathway diagram and updates the Details Panel to show details of the reaction. If the reaction is not in the visible region of the diagram, the view will re-centre and zoom to show it. If instead of clicking an event, you hover the mouse pointer over its name, it will be highlighted in yellow. In the figure above, the sub-pathway Platelet calcium homeostasis is highlighted in yellow.

Getting Started

Hierarchy Panel Exercises

This exercise is to check that you understand the organisation of the Hierarchy Panel. You don’t need to look at the Diagram Panel.

From the Home page, search for PDGF signaling.

In the results page, open the expandable hierarchy in the section Locations in the Pathway Browser by clicking on the + button. DON’T click on the location before expanding the hierarchy! This will open the pathway diagram in the Pathway Browser.

Look at the Hierarchy Panel on the left.

  1. How many sub-pathways does this pathway have?
  2. How many reactions are in the first sub-pathway?
  3. What reaction(s) follow ‘Translocation of PDGF from ER to Golgi’? Hint:Look in the Details Panel, bottom-right.  If it is hidden, use the layout buttons in the top right corner, above the diagram, to reveal it.

Subpathway Exercises

This exercise is to check that you understand Subpathway icons and the relationship between the Pathway Hierarchy and Pathway Diagram.

Open the pathway Hemostasis in the Pathway Browser.

Select the subpathway ‘Platelet Hemostasis’.

  1. What happens if you hover your mouse pointer in the Hierarchy on the sub-pathway ‘Platelet calcium hemostasis’?
  2. What happens if you click in the Hierarchy on the sub-pathway ‘Platelet calcium hemostasis’?
  3. What happens if you click in the hierarchy on the reaction ‘Binding of ATP to P2X receptors’?

More Information

There are 5 subtypes of reaction node, indicating reaction subclasses.

  • Open squares represent ‘transition’, i.e. a change of state that is not one of the defined subclasses.
  • Solid circles represent ‘association’, i.e. binding
  • Double-bordered circles represent ‘dissociation’
  • A square with two slashes represents an ‘omitted process’. This is used when the full details of a reaction have been deliberately omitted. This is most commonly used for events that include representative members of a large family to illustrate the general behaviour of the group. It can be used for reactions that occur with no fixed order or stoichiometry, or for degradation events where the output is a random set of fragments.
  • Squares containing a question mark represent an ‘uncertain process’, where some details of the reaction are known, but the process is thought to be more complex than represented. Explanatory details are typically included in the Description.

Reaction Node Exercises

This exercise is to check that you understand reaction node subtypes.

From the Home page, search for the pathway ‘Effects of PIP2 hydrolysis’ and open it in the Pathway Browser (in any of the several locations)

  1. What symbol represents the reaction for ‘Binding of IP3 to the IP3 receptor’?
  2. What symbol represents the reaction ‘IP3R tetramer:I(1,4,5)P3:4xCa2+ transports Ca2+ from platelet dense tubular system to cytosol? What subtype of reaction is this?
  3. Open the subpathway ‘Arachidonate production from DAG’. What is the name of the catalyst for ‘2-AG hydrolysis to arachidonate by MAGL’? Can you name the three outputs of this reaction?
  4. Can you find the UniProt ID for the catalyst? Hint: There are several ways to find this, two require you to select something!