- 1 Introduction
- 2 What is Reactome?
- 3 The Reactome Front Page
- 4 The Pathway Browser and Tools
- 4.1 The Pathway Browser
- 4.1.1 Pathways Overview Display
- 4.1.2 Pathway Hierarchy Panel
- 4.1.3 Pathway Diagrams
- 4.1.4 Navigating Pathway Diagrams
- 4.1.5 Details Panel
- 4.1.6 Context Sensitive Menus in Pathway Diagrams
- 4.1.7 Navigating Disease Pathway Diagrams
- 4.1.8 View Equivalent Pathway In Another Species
- 4.1.9 Molecular Interaction Overlay
- 4.1 The Pathway Browser
- 5 Searching Reactome
- 6 Reactome Tools
- 6.1 Pathway Analysis
- 6.2 Species Comparison
- 6.3 Pathways Overview and Analysis Results
- 6.4 FI Network Tool
- 7 Download Reactome
- 8 Exporting Data From Reactome
This document is an overview of the Reactome database of biological pathways and processes and its web site. This is not a comprehensive guide, but should provide you with enough information to browse the database and use its principal tools for data analysis. Please read through it and contact us with any comments or questions.
To explain some of the terms used in this User Guide, we have created a Glossary.
What is Reactome?
Reactome is a curated database of pathways and reactions (pathway steps) in human biology. The Reactome definition of a 'reaction' includes many events in biology that are changes in state, such as binding, activation, translocation and degradation, in addition to classical biochemical reactions. Information in the database is authored by expert biologist researchers, maintained by Reactome editorial staff, and extensively cross-referenced to other resources e.g. NCBI, Ensembl, UniProt, UCSC Genome Browser, HapMap, KEGG (Gene and Compound), ChEBI, PubMed and GO. Inferred orthologous reactions are available for over 20 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, Arabidopsis and E.coli.
The Reactome Front Page
This is the normal entry point for most users of Reactome. To view this page, type: http://www.reactome.org into the URL slot on your browser.
This page is divided into six parts:
- The Banner contains a Reactome icon in the banner, which is interactive and when clicked from elsewhere within the website will bring the user back to the homepage.
- The Navigation Bar just below the banner has drop down menus giving access to data and functionality available on the Reactome website.
- Six Tool Buttons on the left-hand side of the page provides shortcut buttons to the most popular analysis tools and downloadable Reactome datasets.
- The Main Text section includes a description of Reactome, the participating research institutions and our funding sources.
- The Twitter feed box on the right-hand side provides up-to the minute Reactome news and a user feedback system.
- The Homepage footer that lists all the webpages accessible throughout the Reactome website.
Most Navigation Bar items are drop down menus. It is found on many pages of the Reactome website. Links from the Navigation Bar include:
- About: Background information such as a description of Reactome and the people involved.
- Content: An overview of the Reactome database, the areas of biology we cover, our plans for content expansion, the structure of our data, and statistics about the current content.
- Documentation: Includes this User Guide, plus technical aspects of Reactome's functionality and data.
- Tools: Tools in addition to those linked as shortcut buttons on the Sidebar. Some of these tools are covered in more detail in the Reactome Tools section.
- Community: Details of Reactome training, publications and representation at conferences and workshops.
- Download: Links to a page where Reactome data and code is available in various formats. See below for more details.
- Contact Us: Opens a form page, which allow you to send your questions or comments to the Reactome helpdesk.
- Search: Type in text (words) or identifiers to locate them in Reactome. For details see Searching Reactome section. Search Examples are listed within the Search text box.
The Six Tool Buttons
The Six Tools Buttons provides easy access to tools, the lower has shortcuts to popular Downloads, Featured tools, and Help. From top to bottom, the features are:
- Browse Pathways: Directly access the Reactome Pathway Browser; see The Pathway Browser and Tools
- Analyze Data: Directly access the most popular Reactome tools; see Reactome Tools for detailed descriptions.
- Reactome FI network: Link to a page describing how to install and use the Reactome Functional Interaction (FI) Network plugin; more details can be found at FI Network Tool
- User Guide: Access this User Guide.
- Downloads: Popular Reactome data downloads.
- Contact Us: Send feedback to Reactome or ask us a question.
The Main Text
This is the text area under the Six Tool Buttons, to the right of the Twitter feed. This area contains the following:
- About Reactome: A one paragraph statement linked to more detailed information.
- Participating Research Institutions: Reactome is a collaboration amongst OICR, NYUMC, CSHL and EBI.
- Funding Agencies: Acknowledging the different funding agencies that support the Reactome project.
The Pathway Browser and Tools
The Pathway Browser is the primary means of viewing and interacting with specific pathways. It includes a search tool, interactive pathway viewer and set of tools for several types of analysis including:
- 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 data from external databases or user-supplied data onto a pathway.
- The display of context-sensitive information from other resources, using widgets provided by the external resources.
The Tool bar on Reactome's Homepage gives access to extended versions of these tools that query across all Reactome pathways (see Reactome Tools).
The Pathway Browser
The Pathway Browser is launched by clicking the Browse Pathways button on the Homepage:
Features of the Pathway Browser are labelled in the diagram below:
- The Features bar across the top of the Pathway Browser has the following items:
- The Reactome logo is a shortcut button that returns you to the homepage.
- Species Selector – Reactome is primarily a database of curated human biological pathways. These human pathways are used to computationally infer equivalent pathways in model organisms (described here). Use the Species Selector to view the pathways inferred for the selected organism. Infectious disease pathways that involve pathogen proteins interacting with human proteins are listed under Homo sapiens.
- Show/Hide toolbar – The pathway browser is divided into 3 main sections. These are 1) the Pathway Hierarchy, on the left, 2) the Details Panel, bottom right, 3) the Diagram Panel, top right. The Show/Hide Toolbar allows you to show or hide these panels.
- Analyse Data – Opens a panel where analyses can be performed
- Quick Tour – click here for a short introduction to Reactome’s key features.
- Diagram Key – this mini key shows the most common objects present in pathway diagrams. Click on the downward-pointing arrow to reveal a more extensive key to pathway diagram features.
- Pathway Hierarchy Panel. The hierarchy of Reactome pathways is listed in the panel on the left side. Similar to the Windows File Manager, sub-pathways can be revealed by clicking on the + symbol to the left of the pathway name. Click on and drag the grey line, separating the Hierarchy panel from the Pathway Diagram Panel, will adjust the width of the Pathway Hierarchy Panel.
- Pathway Diagram Panel. This is where pathway diagrams are displayed, when selected in the Pathway Hierarchy Panel. The Pathway Diagram panel will display a brief guide to the pathway browser until you select a pathway. Top-left of this panel is a navigate/zoom tool. Click on the arrows to move across the diagram. The ‘double arrow” button resizes the pathway diagram to fit the available space. Click on the ‘+’ or ‘-‘ buttons to zoom in and out, respectively. The mouse scroll wheel also zooms.
- Tabbed Details Panel. It gives details of the selected pathway, reaction, complex, set or proteins, when they are selected in the pathway diagram or Pathway Hierarchy panel. This panel can be revealed/hidden using the small yellow triangle on the border with the Pathway Diagram panel. Selecting a location in the pathway diagram with your cursor, and scrolling the wheel will zoom in/out wherever the cursor is located.
Pathways Overview Display
Pathways Overview provides an intuitive visual overview of the Reactome hierarchical pathway structure, and the results of pathway analysis using Reactome tools.
The Pathways Overview is a genome-wide, hierarchical visualization of Reactome pathways in a space-filling graph. Each node represents a pathway, and the size of the node reflects the number of entities (proteins, small molecules, genes, etc) belonging to that pathway. The edges represent the connection between the different pathway nodes within the Reactome pathway hierarchy. The central node within each pathway burst is the parent (or top-level) pathway node. Each child (or sub level) pathway belonging to the pathway hierarchy is represented as a node, which is projected outwards from the central node and connected to the subsequent pathway in the hierarchy, until the lowest level pathway is reached. When the graph initially loads, the Pathways Overview display automatically fits all the nodes and edges into the existing area.
There is a navigation tool top-left of the Pathways Overview display. With this it is possible to navigate left, right, up or down and zoom in or out of the diagram. It also allows zooming using the mouse wheel, and click and drag the diagram.
Touchpad and mouse wheel actions allows zooming in or out (relative to the mouse position). The level of zoom in and out also takes into consideration the scrolling speed of the mouse wheel/touchpad action. For example, a strong movement of the wheel accelerates the zooming (in or out) to quickly show the final zoom level. On the other hand, slower mouse wheel/touchpad scrolling will produce more subtle changes within the level of zoom.
Moving the mouse while keeping the left button pressed moves the viewport, so hidden areas can be displayed. Depending on the level of zoom, more or less information is shown on the screen next to the nodes just to avoid a crowded view.
Clicking the “show all ( )” icon adjusts the view to show all the nodes and edges in the available area within the display panel.
If a particular node is selected, clicking the “open selected pathway” icon, to the right of the navigation arrows, will change the display panel to show the selected pathway diagram. Double clicking or clicking an already selected node (or its pointing edge) will open the pathway diagram.
From the pathway diagram view, it is possible to return to the Pathways Overview display, by: i) clicking the "Pathways Overview” button located in the bottom right corner of the pathway diagram, ii) zooming out either with the mouse wheel or iii) clicking the zoom-out button in the diagram control panel.
Located at the top right of the Pathways Overview display is the ”settings button”, which will provide the following two options:
- Colour profiles: presents a list of colour profiles (named after "the science behind fireworks"). Each of them offers different combinations for the standard view and the results of the molecular and expression overlays.
- About Pathways Overview: shows a window with a short explanation about the widget.
Selecting a pathway in the hierarchy panel will highlight the name of the pathway, zoom in and centre upon the selected pathway in the Pathways Overview display, and update the information displayed in the details panel. If the selected pathway is not currently visible in the viewport (or not centred), it will be automatically re-centred with an appropriate level of zoom to display all nodes and edges of the connected parent pathways.
Selecting a pathway node in the Pathways Overview panel will overlay the name of the pathway in blue text onto the display, and provide information about that pathway in the details panel. When the text associated with the pathway node is not shown or is too small to read due to the level of zoom, hovering over a node displays a tooltip with the name of the pathway. Hovering over an edge will highlight it and the preceding nodes and edges all the way up the pathway hierarchy to the parent node(s).
The thumbnail, in the bottom-right corner of the Pathways Overview display, is a smaller representation of the space-filling graph. When the view is zoomed in, the white box within the thumbnail represents the current display in the viewport. If the visible area changes either because of a zoom level adjustment or the area for the display changes, the size of the white box in the thumbnail adjusts to reflect the change in the viewport. Clicking and dragging the white box will reposition the viewport, so it can be used to quickly navigate to the region of interest.
Highlighted nodes and edges are also visible in the thumbnail either those are in the white area or outside, so it is possible to identify the location of the objects before focusing on them. This is particularly useful when using the event hierarchy to transition from an area of focus to a region outside the current viewport.
To view the predicted conservation of the human graph display in another species, use the "Switch Species" drop-down menu at the top of the Pathway Browser. Selecting causes the Pathways Overview panel to re-draw. The layout of the Pathways Overview display is preserved, but any pathways that were not inferred will be absent. The event hierarchy is also updated to display the events present in the selected species. The size of the pathway nodes will change from species to species due to the ortholog projection process.
When the species Gallus gallus, Mus musculus and Mycobacterium tuberculosis are selected (these species have both manually curated and computationally inferred pathways in Reactome), the Pathways Overview panel will display both inferred and manually curated pathways. The latter set of pathways will appear visually to the right in the Pathways Overview display and textually in the pathway Hierarchy panel at the bottom. As you navigate within these inferred and manually curated pathways, you can select individual pathway nodes and see their descriptions in the Details panel.
A helpful feature of the graph display is how it shows how some of the sub pathways in Reactome are shared between different top-level pathways. For example, the RAF/MAP kinase cascade is a sub pathway of the Signal Transduction, Developmental Biology, and Immune System.
Pathway Hierarchy Panel
This contains a list of Reactome pathway topics, sorted alphabetically. Some topics, such as apoptosis, are too large to represent as a single pathway. Instead they are divided into sub-pathways, which may be further divided into sub-pathways. Most Reactome pathway topics are divided into smaller sub-pathways. Individual steps in a pathway are known as reactions. The organisation of pathways, sub-pathways and reactions is represented on the Pathway Hierarchy panel as a pathway hierarchy. This view functions in a similar manner to the Windows File Manager; sub-pathways are revealed by clicking on the + symbol to the left of the pathway name, and hidden by clicking on the – symbol. The ‘U’, ‘N’ and ‘+’ icons to the left of the pathway name identify whether a pathway is Updated, New or associated with Disease.
Pathways and reactions can be differentiated by a representative symbol to the left of the name, see the image Pathway Hierarchy Symbols below. You may also see a symbol representing 'black-box' reactions, where complete details have been omitted as unnecessary or are not completely determined.
Within a pathway, the order of reactions in the hierarchy from top to bottom usually follows their order in the pathway, so that preceding reactions are above the subsequent reaction, but note that this is not always the case. Reactome has a more formal way of identifying connected reactions called Preceding and Following Events, visible in the Reaction Details (see Details Panel below).
Pathway diagrams represent the steps of a pathway as a series of interconnected molecular events, known in Reactome as 'reactions'. Reactions are the core unit of Reactome's data model. They encapsulate 'changes of state' in biology, such as the familiar biochemical reaction where substrates are converted into products by the action of a catalyst, but also include processes such as transport of molecules from one cellular compartment to another, binding, dissociation, phosphorylation, degradation and more. Cellular compartments are represented as pink boxes - a typical diagram has a box representing the cytosol, bounded by a double-line that represents the plasma membrane. The white background outside this represents the extracellular space. Other organelles are represented as additional labelled boxes within the cytosol. Molecules 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 molecule on the boundary of the cytosol is in the plasma membrane.
A "pop out" diagram key is found in the upper right corner of the webpage.
The diagram key provides a descriptions of the icons used in the diagrams:
Objects on the diagram represent reaction inputs and outputs, and the catalyst if relevant (see A below).
Reactions typically include:
- Inputs, outputs and catalysts, represented as boxes or ovals.
- Green ovals are small molecules or sets of small molecules.
- Green boxes with rounded off corners are individual proteins or sets of proteins or mixed sets.
- Green boxes with square corners are proteins that have no Uniprot accession (or did not at the time the reaction was created).
- Blue boxes are complexes, i.e. proteins and/or small molecules that are bound to each other.
- Green boxes with white inner boxes are sub-pathways.
- Input and output molecules are joined by lines to a central 'reaction node' (surrounded by a green box in Reaction Objects 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.
- Numbered boxes on the line between an input/output and the reaction node indicate the number of units of this input/output in the reaction (when n >1).
- Reaction input/output molecules are often connected by arrows to molecules that take part in 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 an open circle.
- 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 are connected to the set object by a line of short dashes.
- Sets with overlapping content are connected by a line of long dashes.
- Reactions that represent a disease process use red connecting lines. Objects associated with a disease state are bordered in red.
The reaction node has 5 subtypes, indicating subclasses of reaction (see Reaction Objects C, below):
- Open squares represent a 'transition'
- Filled circles represent 'association', i.e. binding
- Double-circles represent 'dissociation'
- Squares with two slashes represent 'omitted process'. This is used to denote a reaction where the full details have been deliberately omitted. This is most commonly used for events that include specific members of a protein family to illustrate the general behaviour of the larger group. It is used for reactions that occur with no fixed order or stoichiometry, and for degradation where the output is a random set of peptide fragments.
- Squares containing a question mark represent 'uncertain process', where some details of the reaction are known, but the process is thought to be more complex than it is represented. Explanatory details are typically included in the Summation section, described here.
The Pathway Diagram, Hierarchy and Details Panel are interactively connected. Clicking on a pathway or reaction name in the Pathway Hierarchy causes it to be highlighted in dark blue, opens the corresponding pathway diagram in the Pathway Diagram panel and populates the Details panel. If the pathway is a sub-pathway, the name of its parent will be highlighted in pale blue.
Selecting a reaction or pathway in the diagram will highlight it in the Hierarchy, and update the information seen in the Details Panel. If the selected event or molecule is not currently visible the pathway diagram will automatically re-centre on the selected object(s). Selecting a molecule in the diagram will produce details for that molecule in the Details Panel.
Where a subpathway is contained within the diagram that is already displayed, clicking on the sub-pathway name in the hierarchy will cause all the reactions in that pathway to be highlighted in blue.
Highlighted reactions are also visible in the thumbnail diagram and can be used to navigate quickly to the region of interest in the diagram using the thumbnail window, bottom left of the Pathway Diagram. The blue box outline represents the current view. Click and drag blue box will reposition the pathway diagram. To centre the diagram at the point, click outside the blue outline. Moving the cursor out of thumbnail box while dragging will stops the pathway repositioning.
Hovering over a protein, complex or small molecule node shows a tooltip with node's name and type. An information icon to the top left of the node is displayed. Clicking the ‘info’ icon will display a context sensitive menu, providing access to more information about the pathway node.
There is a navigation tool top-left of the Pathway Diagram. With this you can navigate left, right up or down and zoom in or out of the diagram. You can also zoom using the mouse wheel, and click and drag the diagram.
Located at the top right of the Pathway diagram is the Pathway Options button, will display the pathway diagram settings, allowing the user to configure different aspects viewing the pathway diagram and to download the pathway diagram.
Large topics such as apoptosis contain too much information to be displayed as a single pathway or diagram. Where this is the case, the topic is divided into sub-pathways in the pathway hierarchy, and sub-pathway diagrams in the Pathway Diagram Panel. If you select a pathway in the Pathway Hierarchy panel that only has sub-pathways diagrams, the Pathway Diagram displays an overview diagram, containing boxes with green borders, the symbol for a sub-pathway diagram. This symbol indicates that a detailed diagram is available but is not part of the currently displayed Pathway Diagram. The sub-pathway diagram symbol can also be used within a pathway diagram if the details of a sub-pathway are too complicated for inclusion, to indicate that the sub-pathway has it's own, separate diagram.
There are two ways to access a sub-pathway diagram. The simplest is to right-click on the sub-pathway diagram symbol. This produces a menu, select the option 'Go To Pathway'. Alternatively, left-click to select the sub-pathway diagram symbol - the corresponding sub-pathway name will be highlighted on the Pathway Hierarchy panel. In the example shown below, the sub-pathway diagram symbol for 'Extrinsic Pathway for Apoptosis' is selected (boxed in blue) causing the corresponding sub-pathway and it's parent pathway to be highlighted blue on the Pathway tab. The sub-pathway name has not been clicked (that would open the diagram for the subpathway) . Clicking on the sub-pathway name in the hierarchy causes the corresponding pathway diagram to open in the Pathway Diagram panel.
The Details Panel is at the bottom of the Pathway Browser. It gives details of the selected pathway, reaction, complex, set or proteins, when they are selected in the Pathway Diagram or Pathway Hierarchy panel. The height of the Details panel can be adjusted by clicking on and dragging the grey line, separating the Details Panel from the Pathway Diagram, to the intended height.
The different tabs within the “Details" panel, provides alternative displays of graphical and textual information depending on whether a pathway, reaction, or physical entity node is selected:
- Overview: Displays summary information relating to the selected pathway, reaction or entity.
- Molecules: This tab contains a List button which displays details of the molecules associated with the event or object selected in the pathway diagram, including links and accession numbers in various external databases. Molecule information can be downloaded as a csv, tsv, xml or excel file.
- Structures:The content displayed in this tab depends on the type of object or event selected in the pathway diagram. For Reactions it will display equivalent reaction diagrams from the Rhea database when available. For Proteins or pathway objects that represent sets or complexes, corresponding structure information from PDBe is represented if available. For simple molecules, the structures tab represents information from the ChEBI database.
- Expression: Displays condition-specific gene expression data from the Gene Expression Atlas.
- Analysis: This tab displays the results of analyses – see the section covering Reactome Analysis Tools for further details.
- Processes: Events and molecular objects in Reactome are re-used if they can take part in more than one process. You can identify the involvement of a molecule or event in multiple processes by referring to the Processes Tab.
- Download: Allows users to download a variety of compatible with third-party tools
Pathway Details Panel
The Overview tab of the Pathway Details Panel typically includes, the pathway name, the species, a stable identifier, a description of the pathway (summation), the GO biological process term for the pathway, the GO cellular compartment term (if applicable), and PubMed references providing background information and experimental support for the pathway.
If the pathway is not supported directly by human experimental data but has been inferred from another species, this is indicated by the phrase 'This event is deduced on the basis of event(s)' and a link to the supporting pathway. The ‘Computationally inferred to' drop down menu lists species that have been computationally predicted to have the same pathway.
The names of authors and reviewers that contributed to the curation, review and/or updating of the pathway are also provided.
Clicking the ‘+’ or ‘-‘ icon associated with the different displayed fields within the Overview tab will show or hide more information about those fields.
The molecules that participate in a pathway can be displayed and/or downloaded by clicking on the ‘Molecules’ tab of the Pathways Details Panel. The user can select the type(s) of molecules to download, the type of information desired for each molecule type, and the format of the download file.
The 'Expression' tab displays gene expression data derived from transcription profiling of combined individuals and a mixture of RNA from 16 human tissues(Illumina Body Map). The heat map employs a two-dimensional matrix where rows correspond to genes (encoding pathway components) and columns correspond to 16 human tissues, such as adipose, brain, colon, etc. Filled boxes indicate genes expressed. A user will be able to see the Expression profiles from the Expression Atlas for all protein participants in the reaction, or the selected entities. Clicking 'Display levels' will show expression values. A human anatomogram provides a graphical display of the gene expression data as a user clicks on the different tissues or gene expression data presented in the table. Clicking the gender symbols denoting male and female will update the anatomogram with sex-specific gene expression data.
The user can select to display the other Reactome pathways for the selected sub-pathway by clicking the Process tab. Clicking a ‘+’ or ‘-‘ icon next to ‘Involved in pathways’ within the Process tab will show or hide more information about the associated pathway and literature citations.
The Download tab provides options for the user to download different files types for the selected pathways. These files include:
- SBML: An exchange format used by systems biologists for their models.
- SBGN: An exchange format used to represent pathway and network diagrams.
- BioPAX2: An exchange format used by systems biologists for their models.
- BioPAX3: An exchange format used by systems biologists for their models.
- PDF: Text dump of the pathway, organized to look like a research report.
- Word: A document format compatible with Microsoft and other word processor software.
- Protege: A format used for ontology exchange.
SBML, SBGN and BioPAX are exchange formats of interest to bioinformaticians. Word and PDF are familiar document formats, providing you with a convenient "document" of the pathway. Protégé is an extensible, platform-independent environment for creating and editing ontologies and knowledge bases, this download is likely to be of interest to those wishing to extend Reactome functionality.
The complete Reactome textbook of biological processes in PDF or RTF format, the complete set of human reactions in Reactome (in SBML or BioPAX level 2 or 3 format), and a list of human protein-protein interaction pairs are available to download from the Download page, linked to the Menu Bar on the Reactome homepage.
To find out about how Reactome generates SBML, see SBML At Reactome.
Reaction Details Panel
Included in the Overview tab of the Reactions Details Panel is a reaction name, a stable identifier, and a summary of the reaction. Reactions must contain literature references that contain experimental data verifying the reaction, or an 'Inferred From' link if the reaction has been manually inferred from experimental data from model organisms. For pathway details see the previous section.
Other details within the Overview section include:
- Input/Output: Identifies the input/output molecules, sets or complexes for this reaction. Icons to the right of these named items link to further information in Reactome.
- Authors: The expert biologists that contributed materials that allowed this reaction to be created in Reactome.
- Reviewers: The expert biologists that verified the content for this pathway.
- Preceding event(s): A list of events that occur immediately before the event being viewed.
- Following event(s): A list of events that occur immediately after the event being viewed.
- Catalyst (when relevant): The protein or complex that catalyzes the reaction. The Gene Ontology molecular function term that represents the activity of a catalyst or transporter within the reaction will be listed. If the catalyst is a complex, the component, or domain in a simple catalyst, that enables the reaction to occur will be listed.
- Inferred from another species (when relevant): This indicates that event has not been experimentally demonstrated in humans, but has been inferred on the basis of data acquired for another species. The link points to a web page containing the experimental data for the reaction in that species.
- Positively (or Negatively) regulated by: The protein or complex that regulates the reactions.
- References: The research publications that describe the evidence supporting the reaction, each hyperlinked to its PubMed abstract (when applicable).
- Taxon: The species in which the event occurs.
- Computationally inferred to: Links to descriptions of the events in other species that are either confirmed to occur in a very similar way in both species, or have been electronically inferred .
The molecules that participate in a reaction can be displayed and/or downloaded by clicking on the ‘Molecules’ tab of the Reaction Details Panel. The user can select the type(s) of molecules to download, the type of information desired for each molecule type, and the format of the download file.
The 'Expression' tab displays gene expression data derived from the Illumina Body Map for the proteins associated with the selected reaction.
The user can display the other Reactome pathways for the selected reaction by clicking the Process tab. Clicking a ‘+’ or ‘-‘ icon next to ‘Involved in pathways’ within the Process tab will show or hide more information about the associated events and literature citations.
Protein, Small Molecule, Complex and Set Details
The details of any protein, small molecule, complex or set represented in a pathway diagram can be displayed in the Details panel by selecting the object within the diagram. These views are all very similar, an example of protein details is represented below. Clicking a ‘+’ or ‘-‘ icon associated with the different displayed fields within the Detail panel tabs will show or hide more information about the protein, small molecule, complex and set.
The Overview tab displays the following information depending upon whether the selected node is a:
- Link to corresponding entries in other databases: Cross-reference to identifiers used for this molecule in external reference databases, with hyperlinks to the record.
- Cellular compartment: The cellular compartment that contains this molecule, with hyperlink to the corresponding GO term.
- Computationally inferred orthologues: Lists equivalent molecules in other species if these have been inferred to exist. A description of the inference process can be found here.
- Components: If this molecule is part of any complexes, they are listed here
- Produced by: If this molecule is 'created', e.g. becomes incorporated into a complex or degraded, the appropriate reactions are listed.
- Consumed by events: If this molecule is 'consumed', e.g. becomes incorporated into a complex or degraded, the appropriate reactions are listed.
- Post-translational modification: If this molecule exists within Reactome in an alternate, post-translationally modified form, the appropriate molecules are listed.
The ‘Molecules’ tab displays more information and link outs to external bioinformatic resources. The user can select the type(s) of molecules to download, the type of information desired for each molecule type, and the format of the download file.
The ‘Structures’ tab will displays 3D structural data and citations from PDB. The most relevant (best) crystal structure for the selected node will be shown. Clicking the "All structures..." will display other associated crystal structure. Users can also explore additional crystal structure infromation at PDB by clicking the different icons:
- Book: A paper describing the PDB entry.
- Person/Multi-Cladogram: The taxon or source of the biomolecule.
- Circular plasmid/Multi: The expermental technique used to create the crystal.
- NMR/X-RAY: The technique used to determine the 3D structure.
- Protein Domain: The protein sequence and domain information associated with protein.
- DNA helix: Nucleic acids (DNA, RNA) are associated (green-highlighted) or not associated (grey-highlighted) with the crystal structure.
- Benzene ring: Ligand is associated (green-highlighted) or not associated (grey-highlighted) with the crystal structure.
The 'Expression' tab displays gene expression data derived from transcription profiling of individual and mixture of 16 human tissues RNA (Illumina Body Map). The heat map employs a two-dimensional matrix where rows correspond to genes (encoding pathway components) and columns correspond to 16 human tissues, such as adipose, brain, colon, etc. Filled boxes indicate genes expressed. Click 'Display levels' to show expression. A human anatomogram provides a graphical display of the gene expression data as a user clicks on the different tissues or gene expression data presented in the table. Clicking the gender symbols denoting male and female will update the anatomogram with sex-specific gene expression data.
The ‘Process’ tab shows the Reactome events associated with the selected node. Clicking the ‘+’ or ‘-‘ icon next to ‘Involved in pathways’ will show or hide more information about the associated events and literature citations. "Is present in sets" displays information about the Reactome sets that the selected node participates in.
Context Sensitive Menus in Pathway Diagrams
Within pathway diagrams, hovering on a node will display an information icon, which when clicked will display a context sensitive menu. Alternatively, right-clicking on the box representing a molecule, complex, set or reaction presents the user with a menu or list of features dependent on the nature of the item selected. Note that unavailable options do not appear, so very few items will have the full range of options.
A context sensitive menu is engaged when a user clicks on the the pathway diagram background (space between nodes and reactions). This menu allows the user to explore additional features of the pathway diagram. Some of these features from this menu are also accessible from the Pathway option tool button that is accessible from the top-right corner of the pathway diagram.
Right-click Menu Items associated with Pathway Nodes
- Other Pathways
- Lists other pathways that include the selected item as a participant. Clicking on any of the pathway names will display that pathway in the Pathway Diagram Panel.
- Display Interactors
- Surrounds the selected diagram item with a set of boxes representing protein-protein or protein-small molecule interactors. For more information see Molecular Interaction Overlay. N.B. Interactors can only be displayed for individual proteins, not for complexes or molecule sets.
- Hide Interactors
- Removes interactors from the selected diagram item, unless it is an interactor of another item in the display. For more information see Molecular Interaction Overlay
- Export Interactors
- Exports all interactors of the selected diagram item from the pre-selected source interaction database and displays them in a new browser tab/window. Interaction data is displayed in PSI-MITAB format. For more information see Molecular Interaction Overlay
- Participating Molecules
- Lists the component molecules for the selected item, e.g. lists the proteins that make up a complex. Clicking on any molecule in that list will open a new window with details.
- Display Participating Molecules
- This popup menu item is displayed following Species Comparison or Expression Analysis. It causes the display of a grid of cells that represent the components of the set or complex. See the relevant sections of the User Guide for more details.
- Go To Pathway
- Associated with symbol for sub-pathway diagrams, selecting this from the popup menu causes the sub-pathway diagram to be displayed. See Sub-pathway Diagrams
Right-click Menu Items associated with Pathway Diagram
This menu is engaged when a user clicks on the the pathway diagram background (space between nodes and reactions). This menu allows the user to explore additional features of the pathway diagram.
- Search Diagram (ctrl-f)
- A user can search for a word or phrase within the nodes and reactions of the pathway diagram. The search tab appears with by pressing the 'ctrl-f' key combination. See Search Pathway Diagram
- Snapshot Current View
- Permits the user to download the current pathway diagram view, including overlays, as a PNG image file that is opened in a new tab.
- Download Diagram
- Allows the user to download the entire pathway diagram, including overlays, as a PNG image file that is opened in a new tab.
- Interaction Overlay Options...
- Opens a pop-up box for configuration of the interaction overlay. For more information see Molecular Interaction Overlay
- Zoom In
- Zoom in within the pathway diagram.
- Zoom Out
- Zoom out within the pathway diagram.
- Center Diagram Here
- In combination with the functions of the mouse scroll wheel, the user can zoom in/out within the pathway diagram, relative to the position of the mouse cursor.
Pathway Options Menu
This button, located on the top-right of the Pathway diagram, opens a control panel that has several functions:
- Search Diagram (ctrl-f).
- Search the diagram nodes and reactions for a word or phrase. The search tab appears with by pressing the 'ctrl-f' key combination. See Search Pathway Diagram for more information.
- Snapshot Current View.
- Take a screenshot of the current pathway diagram view, which will be opened in a new window.
- Download Diagram.
- Will open the entire pathway diagram in a new window, ready for download.
- Interaction Overlay Options…
- Allows configuration of Molecular Interactions onto the pathway diagram.
Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes:
- the inclusion of microbially-expressed proteins
- altered functions of human proteins
- changed expression levels of otherwise functionally normal human proteins
For some Reactome disease pathways, such as "Signaling by EGFR in cancer" it is helpful to describe the effects of disease related reactions and entities on the normal human pathway. In this case, disease related events are overlaid on top of the diagram of the normal human pathway that they affect. This “merged" diagram is viewed by clicking on the disease pathway. Disease related entities and reactions are outlined in red whereas the normal events and entities are “greyed out”. In the event hierarchy, the parent pathway contains the pathway containing the disease associated reactions (Signaling by constitutively active EGFR).
The “normal" subpathway entities and reactions are still live and may be selected within the the ELV. This allows the user to browse the disease and normal events.
The disease reaction nodes are not "greyed" out, indicating that they are part of the disease process. Disease related pathways, reactions, and entities may be flagged, in the details section, with the most relevant EBI Human disease ontology term.
- Note: It is not possible to link to the Human disease ontology website directly from the disease tagged entity/event. This feature will appear in a future release.
Some disease pathways in Reactome are not grouped with a separately annotated "normal" pathway and diagram. These include infectious disease pathways (and the Amyloids pathway) in which the majority of annotated reactions involve pathogen (abnormal) proteins only and/or involve interactions among pathogen (abnormal) and human proteins. These disease pathways that lack a "normal" counterpart do not have any "greyed" out segments within the associated ELV diagrams. Red lines are used to emphasize disease events. Reactions involved in disease or disease progression are highlighted in red as are any entities that are disease-associated or derived from another species (pathogen). Host/human or normal entities are black. Complexes that contain both host and disease associated/pathogen derived entities are colored red.
View Equivalent Pathway In Another Species
Reactome is human-centric and aims to represent human biology. Pathways in other species are electronically inferred from curated human pathways - a description of the inference process can be found here.
To view the predicted conservation of the displayed pathway in another species, use the "Switch Species" drop-down menu at the top of the Pathway Browser. Selecting causes the pathway diagram to re-draw (a revolving arrow icon on the Pathway Hierarchy panel indicates the diagram is re-drawing). The layout of the diagram is preserved, but any reactions that were not inferred will be absent. The event hierarchy is also updated to display the events present in the selected species.
Note however that when the species Gallus gallus. is selected (this species has both manually curated and electronically inferred pathways in Reactome), it is currently only possible to view the manually curated Gallus pathways. To view the electronically inferred Gallus pathways, you must go to a pathway of interest in human and select the electronically inferred Gallus event in the details section. The inferred Gallus pathway diagram will then be displayed, but the manually curated pathways for Gallus will be listed in the event hierarchy. To navigate within these inferred Gallus pathway diagrams, you can select individual reaction nodes or reaction participants and see their descriptions in the details panel.
A more sophisticated method of comparing pathways between species is available as the Species Comparison tool.
Molecular Interaction Overlay
Molecular Interaction (MI) overlay allows protein-protein or protein-compound interactions to be overlaid (superimposed) onto the pathway diagram. The source depends on the currently selected interaction database. The default is IntAct, other sources of interaction data (protein-protein and protein-compound) including a user-supplied list can be selected using the ‘Interactor Overlay Options…’ feature of the Pathway Options button in the top-right corner of the Pathway diagram.
A maximum of 10 interactors are displayed as a ring of blue-bordered boxes connected by blue lines to the selected protein. A white box superimposed onto the selected protein displays the number of interactors up to a value of 50, if more than 50 are identified 50+ will be displayed.
Several items can be sequentially selected for interactor display. If the same interactor is connected to more than one item it is re-used, i.e. connected to all the selected items in the diagram.
- Hovering the mouse pointer over a protein interactor produces a pop-up containing the name and identifier of the protein.
- Hovering over a chemical interactor displays the formula and name of the chemical.
- Clicking on a protein interactor opens the Uniprot entry for that protein in a new window.
- Clicking on a chemical interactor opens up the ChEBI entry for that chemical in a new window.
- Clicking on the line that connects the interactor to the pathway item opens a new window containing details of the interaction at the source database (see example below) ** Please note that link to the source database is not currently working for Internet Explorer 8**.
Details of up to 50 interactors for every protein in the pathway diagram can be viewed as a table accessed via the Analyze, Update & Annotate button. An extended version of this table with no limit to the number of interactors per protein can be exported. See Analyze, Update & Annotate button for details.
While interactors are displayed, right clicking on the selected protein produces two new options, Hide Interactors which removes them, and Export Interactors. Interactions are exported in PSI-MITAB format.
MI Overlay tab
This tab contains the following features:
- Interaction database - a drop-down list allows selection of the source of interactors. This is automatically populated by querying the PSICQUIC Registry. If a new database is selected while interactors are displayed on the pathway diagram, the proteins represented by those items will be used as queries in the new database and the display will automatically update. If the table of interactions is displayed, it will automatically update to list the interactions found in the new database.
- Upload a file - allows a user supplied list to be used as the source of interactors. Data must be in PSI-MITAB format though the only columns that need to be filled in are the accession number, gene name and confidence score columns (confidence score is only necessary if you want to use the color interactions feature). If the upload is successful, the label you submit when prompted will appear on the 'Interaction Database' drop down and can be selected as a source of interactions. A data set submitted in this manner will persist for the user session.
- Clear overlay - removes all interactors from the pathway diagram.
- Submit a New PSICQUIC service - can be used to add a new source interactions database. The URL field should contain the URL of the PSICQUIC service (REST interface). A service added this way will appear on the interaction database drop down for a period of three days, assuming you connect from the same computer.
- Set Confidence Level Threshold - this allows the user to set a confidence threshold used for colouring interactors. The default threshold is 0.5. Interactions with a confidence level below this threshold will be coloured according to the color set as the 'Below' colour, interactions with confidence scores equal to or above the threshold will be coloured with the 'Above' colour.
- Colour button - activates colouring of the pathway diagram - interactions will be coloured only if a confidence score is available at the source database. The colours used can be changed by clicking on the coloured squares for 'Above' and 'Below'. A dialog allows selection of an alternative colour. Click 'Apply' to update the colours displayed.
- Colouring Off button - removes colouring.
The colours used for interaction colouring can be changed by clicking on the coloured squares for 'Above' and 'Below'. A dialog allows selection of an alternative colour, click 'Apply' to update the colours displayed.
- Display/Hide Table of all interactors for pathway - this button switches on/off the table of pathway item-interactor pairs.
- Clicking on the blue 'toggle' squares within this table will cause the pathway diagram to centre on the protein represented in the first column and display its interactors.
- All entries (rows in the table) for that pathway protein will be shaded a pale blue when interactors are displayed. Clicking the toggle for a particular pathway protein a second time will hide the interactors and its table entries will be coloured white.
- Clicking on a pathway protein ID (listed in the second column of the table) will re-centre the pathway diagram on that protein.
- Export all interactors for pathway - exports a full list of interactors for each protein on the pathway diagram, in PSI-MITAB format, as a new window.
Search Pathway Diagram
The Search Diagram (found in diagram options menu) permits the selection of an entity matching the search term and centers the diagram if it is not visible. The "Select All" feature allows for navigation of all entities matching the search query. "Next" and "Back" allows the user to cycle through the diagram search results.
A number of options are available for searching Reactome, depending on your requirements. The "simple search" will be quite sufficient for most users. If you need to make more complex, logical, queries, then you will need to use the Advanced search. The simple and advanced search features are accessible from the top right of the Reactome home page banner and under “Tools” on the Reactome homepage banner, visible from all pages except the Pathway Browser. respectively.
The simple text search tool is located top right of the homepage banner, visible from all pages except the Pathway Browser. Type the word, identifier or accession number and then click on the "Search" button. You will be presented with a results page similar to this:
Results are displayed in a context dependant mannner depending on your query. Results are ordered into the categories: Proteins, Sets, Complexes, Chemical Compounds, Reactions, Pathways, and other entities, if your query matches Reactome annotations. Clicking on the title (URL) will redirect you to go to the corresponding Reactome web page with additional information about your search query. Some results will have descriptive text details, whereas others might link directly to the Pathway Browser. Your search terms will be highlighted if they appear within the title or descriptive text.
By default, the results are displayed for human species and entries that do not belong to a particular species. The latter is relevant to searches involving small molecules.
At the top right of the results page is a set of tick boxes, to filter and refine your search. Selecting one or more of the selector boxes will automatically restrict your search and refresh the search results page. The clicking one or more of the selector boxes will preform the following:
- Species: restrict the search to a particular species.
- Types: display only information relating to Protein, Set, Complex, Chemical Compound, Reaction, Pathway or OtherEntity.
- Compartments: filter your results for a particular cellular compartment(s).
- Reaction types: display results for specific types of reactions.
- Search properties: clustered search.
By selecting a protein link from within the initial search results, the following page will be displayed describing the protein annotations:
By selecting a RNA sequence link, the following page will be displayed describing the RNA annotations:
By selecting a Set link, the following page will be displayed describing the component set annotations:
By selecting a Complex link, the following page will be displayed describing the complex annotations:
By selecting a Chemical Compound link, the following page will be displayed describing the chemical, small molecule and drug annotations:
Within each of these search results pages there are a number of link outs to further information within Reactome and other third party bioinformatics resources. By selecting a Reaction or Pathway link, the user will be redirected to the Pathway Browser displaying the selected pathway diagram.
The Advanced Search form can be accessed under Tools on the Reactome homepage Menu Bar, visible from all pages except the Pathway Browser. This search method supports full Lucene QueryParser syntax including:
- Quotation marks for exact searches and brackets for grouping terms together
- Boolean operators: 'AND', 'OR', 'NOT', '+' and '-'
- Wildcard operators: '?' and '*'
- Proximity matching: "raf map"~4 will search for raf and map within 4 words from each other
There is also the possibility of specifying the field you want to search in with, such as: dbId, stId, name, type, species, synonyms, summation, compartmentName, compartmentAccession, goBiologicalProcessName, goBiologicalProcessAccession, goCellularComponentName, goCellularComponentAccession, goMolecularFunctionName, goMolecularFunctionAccession, literatureReferenceTitle, literatureReferenceAuthor, literatureReferencePubMedId, literatureReferenceIsbn, crossReferences, referenceCrossReferences, referenceName, referenceSynonyms, referenceIdentifier, referenceOtherIdentifier, referenceGeneNames. The syntax for this field-specific query is fieldname:searchterm.
To make full use of the Advanced Search we recommended that you read the document Data Model (available under Documents from the Menu Bar on the Reactome homepage) and refer to the Database Schema (linked to the Data Model document and under Contents from the Menu Bar).
This example provided in the Advanced search form page will identify Reactome annotations, across all species, with names that include the words "raf" and "map" or "PTEN S170N", "apoptosis" or the stable identifier "REACT_12858.1". By selecting different "Filtering Parameters", the query can be refined to display specific information.
Small Molecule Search Tool
This is accessed via the Menu bar on the Reactome homepage, select Tools, Small molecule Search. This will open the Small molecule search page where you can specify the small molecule by name or by structure. Structures can be hand-drawn, or pasted as a SMILES string. Options include search for molecules that contain this structure or those that resemble this structure. Click on the Search button to start the search. The tool will search the ChEBI database. A list of matching compounds is returned, with links to the appropriate Reactome pathways.
Author/Reviewer Search Tool
Reactome depends on collaboration between our curation team and outside experts to assemble and peer-review its pathway modules. The integration of ORCID within Reactome enables us to meet a key challenge with authoring, curating and reviewing biological information by incentivizing and crediting the external experts that contribute their expertise and time to the Reactome curation process. More information is available at ORCID http://orcid.org and Reactome.
This is accessed via the Menu bar on the Reactome homepage, select Tools, Author/Reviewer Search. This will open a web page entitled "Query your pathway contributions in Reactome" This tool allows users to query the Reactome database for their pathway contributions, and download their contributions as a citation for importation into ORCID.
This tool allows searching for author/reviewer by name or email address, which returns the contributor’s ORCID ID, if available, and links to all pathways the person has either authored or reviewed.
The tool also offers links for creating or reporting ORCID IDs and functionality to export author contributions in BibTeX format suitable for importing to the person’s ORCID account.
The Pathway Analysis Portal combines a number of analysis and visualization tools to permit the interpretation of user-supplied experimental data sets. This portal is launched by pressing the "Analysis-Magnifying Glass" Button in the Feature Bar of the Pathway Browser, the "Analyze Data" button on the homepage, or the "Analyze Data" link from the "Tools' drop-down menu.
The portal opens a submission form, where you can select the analysis you want to perform, paste in or browse to a file containing your data, or use an example data set. The submission process recognizes many types of identifiers. As part of the pre-analysis, they are mapped to Reactome molecules. The ideal identifiers to use are UniProt IDs for proteins, ChEBI IDs for small molecules, and either HGNC gene symbols or ENSEMBL IDs for DNA/RNA molecules, as these are our main external reference sources for proteins and small molecules. Many other identifiers are recognized and mapped to appropriate Reactome molecules. Accepted identifiers include HUGO gene symbols, GenBank/EMBL/DDBJ, RefPep, RefSeq, EntrezGene, MIM, InterPro, EnsEMBL protein, EnsEMBL gene, EnsEMBL transcript, and some Affymetrix and Agilent probe IDs.
Uniprot isoforms may be specified using the format P12345-2. If the –n suffix is omitted this canonical form and all isoforms of it will be matched. Mixed identifier lists may be used. Identifiers must be one per line. Protein-specific identifiers will typically map to protein entities, while gene-specific identifiers will map to the gene, transcript and derived proteins. If desired results can be filtered to show protein-specific or gene/transcript-specific results, details below.
The initial outputs from the analysis is dependent on the dataset uploaded, i.e. a gene list, non-human vs human data, or an expression dataset.
Gene list Dataset
If the dataset is an user-supplied set of human gene or protein identifiers, the analysis portal performs an enrichment test to determine whether any Reactome pathways are enriched in the submitted data, i.e. it answers the question 'does the list represent the proteins within a specific pathway more than would be expected if the set were random?'. A binomial test is used to calculate the probability. The p-values are corrected for multiple testing (Benjamini-Hochberg procedure) that arises from evaluating the submitted list of identifiers against every pathway.
The initial results of the overrepresentation analysis are displayed as a table in the "Analysis results" tab. Analysis results are shown in the Analysis tab, within the Details Panel. All Reactome pathways are shown, in blocks of 20 pathways, ranked by the FDR value obtained from over-representation analysis. In addition, the number of molecules matched/total number of molecules and FDR values are added to the right side of pathway names in the Pathway Hierarchy Panel. Reactions that contain any of the matching molecules are boxed in orange. When you click on the name of a pathway in the Analysis tab, the Pathway Hierarchy will expand to show it and its name will be highlighted in dark blue. If it has subpathways, you can use the plus buttons to the left of the pathway name to reveal subpathways and reactions. The columns represent:
- Pathway name: Click the name to open the pathway.
- Entities found: the number of molecules of the type selected with Results Type that are common between the sumbitted data set and the pathway named in column 1. Click on this number to display the matched submitted identifiers and their mapping to Reactome molecules.
- Entities total: The total number of molecules of the type selected with Results Type within the pathway named in column 1.
- Entities ratio: The ratio of entities from this pathway that are molecules of the type selected with Results Type Vs. all entities of the type selected with Results Type.
- Entities pvalue: The result of the statistical test for over-representation, for molecules of the results type selected.
- Entities FDR: False discovery rate. Corrected over-representation probability.
- Reactions found: The number of reactions in the pathway that are represented by at least one molecule in the submitted data set, for the molecule type selected with Results Type.
- Reactions Total: The number of reactions in the pathway that contain molecules of the type selected with Results Type.
- Reactions ratio: The ratio of reactions from this pathway that contain molecules of the type selected with Results Type Vs. all Reactome reactions that contain molecules of the type selected with Results Type.
- Species Name: The species name.
Clicking on any of the Pathway Names in the "Analysis results" table launches the Pathway Browser in a new browser tab and displays the relevant pathway diagram (see example below).
Nodes in the pathway diagram are yellow-coloured when a gene within your list matches a protein with the pathway diagram
- Protein Nodes - coloured yellow. Hovering the mouse pointer over a protein node displays the submitted identifier and the expression value.
- Pathway Nodes – coloured yellow in horizontal segments with each segment representing a protein in the pathway
- Set and Complex Nodes - coloured yellow in horizontal segments with each segment representing a component in the set/complex that is a protein. Right clicking on the set/complex icon and select 'Display Participating Molecules'. A popup is displayed representing the set/complex as a table with the component name, expression identifier, and the expression level.
- White nodes represents proteins or small molecules with not matches in the uploaded data set.
Hovering the mouse pointer over a cell displays the name of the protein. Clicking on the cell displays details of the protein in the Details pane. The grid can be closed by clicking the 'x' in the top right corner.
By default, all molecules (protein, small molecules, genes, transcripts) are used for overrepresentation analysis. Subtypes of molecule can be selected from a drop-down list located top-left of the results table. Selecting of these subsets will re-display results that consider only the selected molecular subtype.
Dataset from a Model Organism
By default, all non-human identifiers are converted to their human equivalents. If you want to use non-human identifiers to search a computationally-inferred non-human Reactome pathway, uncheck the box. You may also prefer to uncheck this box if your query consists of a mixture of human and microbial identifiers, representing an infection.
"Project to Human" Pathway Analysis
The results are ready to view when analysis results appear (or are updated if already present) in the Pathway Hierarchy. Clicking on a pathway name launches the Pathway Browser and displays the relevant Pathway Diagram.
The results page is very similar to that seen following submission of a simple one-column list of identifiers.
"Computationally Inferred Non-Human" Pathway Analysis
The results are ready to view when analysis results appear (or are updated if already present) in the Pathway Hierarchy. Clicking on a pathway name launches the Pathway Browser and displays the relevant Pathway Diagram.
The results page is very similar to that seen following submission of a simple one-column list of identifiers.
If you submit data in a format that includes columns of numeric values, following a first column of protein, compound or other suitable identifiers such as probe IDs, the analysis tool will interpret your data as expression data. The numeric values are used to colour objects in pathway diagrams. This view was created for microarray data, but any dataset that consists of a list of identifiers with associated numeric values can be used, e.g. quantitative proteomics, GWAS scores.
The tool is launched using the Analyse data button in the Pathway Browser header bar. Either paste your data into the submission form or browse to a saved file (or select an example file).
The results page is very similar to that seen following submission of a simple one-column list of identifiers, with extra columns in the Analysis details following column 9. These extra columns represent the submitted expression values. Clicking on a pathway name launches the Pathway Browser and displays the relevant Pathway Diagram.
Nodes in the pathway diagram are coloured according to the user-submitted numerical values. The yellow-blue colour range is used to distinguish the expression values, employing a linear spectrum from yellow for the highest values to dark blue for the lowest values. The scale automatically adjusts to fit the numerical range represented in the dataset.
- Protein Nodes - yellow or blue colour depending on expression value. Hovering the mouse pointer over a protein node displays the submitted identifier and the expression value.
- Pathway Nodes – coloured in horizontal segments (from lowest to highest expression level) with each segment representing a protein in the pathway
- Set/Complex Nodes - coloured in horizontal segments (from lowest to highest expression level) with each segment representing a component in the set/complex that is a protein. The value associated with each component of a complex can be viewed; right click on the complex and select 'Display Participating Molecules'. A popup is displayed representing the complex as a table with the component name, expression identifier, and the expression level.
- White nodes represents proteins or small molecules with no numerical data are coloured white.
Hovering the mouse pointer over a cell displays the name of the protein. Clicking on the cell displays details of the protein in the Details pane. The grid can be closed by clicking the 'x' in the top right corner.
The Experiment Browser toolbar (orange bar with pale blue arrows, at the bottom of the Pathway Diagram) allows you to step through the columns of your data, e.g. time-points or disease progression. Move between them by pressing the arrow buttons. The header of the data column (if present) is displayed between the arrows. The pathway diagram will re-colour to reflect the new values.
Reactome uses manually-curated human pathways to electronically 'infer' their equivalents in 19 other species. A full description of the inference process can be found here. The Species Comparison tool allows you to compare human pathways with these predicted pathways, to see what is common to both or perhaps missing in the model organism.
Species Comparison is launched using a button on the sidebar, on the left side of the homepage. On the resulting page is a selection tool that reveals a drop-down list of species.
Choose one and click the Apply button. It may take some minutes before the results appear. The results page will look something like this:
The colour of reaction objects indicates the result of the comparison:
- Yellow indicates that the protein has an inferred equivalent in the comparison species.
- Blue indicates that no equivalent was identified. This protein may not exist in the comparison species.
- White indicates that inference was not possible. This is always the case for small molecules, DNA and other objects that have no UniProt entry (or did not at the time the pathway was constructed).
- Objects with bands of colour represent complexes or sets containing more than one molecule. The bands of colour reflect the inference success for the molecules within the complex/set.
To view species comparison results for a complex or set right click it and select the option Display Participating Molecules. This reveals a table representing all the proteins involved in the complex/set. Each square in the grid represents one component of the complex/set, coloured as described above.
Pathways Overview and Analysis Results
One of the main aims of this project is to offer users an intuitive overview of dataset analysis results in the context of the Reactome hierarchical pathway structure, allowing both a quick “first glance” and rapid zooming in on interesting results.
The Pathways Overview display provides an intuitive view for summarizing the results of the overrepresentation analysis. Nodes and edges are coloured depending on their significance in the overrepresentation analysis. A control panel on the bottom centre of the Pathways Overview panel, contains one button to remove the overlay and return you back the standard Pathways Overview display, and a colour legend on the right hand side.
Based upon the user-selected colour profile, the colours legend show lines depending on the significance values of the selected/hovered node. To compare the levels of significance between two individual nodes within the viewpoint, clicking the first node will affix a line within the legend corresponding to the significance value of the selected node. Moving the cursor, and hovering over the second node will place a second line in the legend reflecting the significance value of the second node. For overrepresentation analysis, if the hovered/selected pathway is not significant, the line does not appear.
Clicking on a pathway name within the overrepresentation analysis results table will change the viewpoint to centre upon the relevant highlighted pathway nodes, and highlight the pathway name in the event hierarchy. Likewise, clicking a pathway name in the event hierarchy will change the viewport to display the highlighted pathway nodes, and highlight the pathway name within the analysis results table.
Expression analysis Section
The Pathways Overview display offers an overview of the results of expression analysis. Nodes and edges are coloured depending on their significance in the expression analysis.
The control panel associated with the expression analysis includes a mechanism to move through the different time series columns manually or automatically by clicking on the "play button". When the time series display is animated, pressing the speed button will change the speed with which the Pathways Overview panel will cycle through each time course result. Please note that the expression analysis overlay also takes into account the pathway significance.
Based upon the user-selected colour profile, the colours legend show lines depending on the significance values of the selected/hovered node. To compare the levels of significance between two individual nodes within Pathways Overview, clicking the first node will affix a line within the legend corresponding to the significance value of the selected node. Moving the cursor, and hovering over the second node will place a second line in the legend reflecting the significance value of the second node. For the expression analysis, if the hovered/selected pathway is not significant, the line does not appear.
Clicking on a pathway name within the expression analysis results table will change the viewpoint to centre upon the relevant highlighted pathway nodes, and highlight the pathway name in the event hierarchy. Likewise, clicking a pathway name in the event hierarchy will change the viewport to display the highlighted pathway nodes, and highlight the pathway name within the analysis results table.
Species Comparison Section
Pathways Overview also provides a useful overview of the species comparison. Nodes and edges are coloured depending on their significance in the species comparison analysis.
A control panel on the bottom centre of the Pathways Overview panel, contains one button to remove the overlay and return you back the standard Pathways Overview display, and a colour legend on the right hand side.
Based upon the user-selected colour profile, the colours legend show lines depending on the significance values of the selected/hovered node. To compare the levels of significance between two individual nodes within Pathways Overview, clicking the first node will affix a line within the legend corresponding to the significance value of the selected node. Moving the cursor, and hovering over the second node will place a second line in the legend reflecting the significance value of the second node. If the hovered/selected pathway is not significant, the line does not appear.
Clicking on a pathway name within the species comparison results table will change the viewpoint to centre upon the relevant highlighted pathway nodes, and highlight the pathway name in the event hierarchy. Likewise, clicking a pathway name in the event hierarchy will change the viewport to display the highlighted pathway nodes, and highlight the pathway name within the analysis results table.
FI Network Tool
- REDIRECT ReactomeFIViz
Exporting Data From Reactome
Reactome content can be exported in a number of different formats. For your convenience, export files for the entirety of Reactome are available in the download section, see Download Reactome for details. The details panel for pathway diagrams also provides a way to do exports for individual pathways or even reactions, take a look at Pathway Details. The following export formats are available:
- SBML. An exchange format used by systems biologists for their models. See SBML At Reactome for comprehensive information about SBML export.
- BioPAX. An exchange format used by systems biologists for their models.
- PDF. Text dump of the pathway, organized to look like a research report.
- Word. Text dump of the pathway, organized to look like a research report. The file generated is of type RTF, and can also be understood by OpenOffice and LibreOffice. *Note: RTF files may be very large, but conversion to Word (or PDF) generates a file that is much smaller with no loss of information.
- Protege. A format used for ontology exchange.
- PSI-MOD. A tabular format containing protein-protein interactions derived from Reactome's reactions and complexes. Take a look at PSI-MITAB Interactions for details.
- MySQL. A database dump of all of Reactome's data. To understand the schema properly, please take look at objectrelational-mapping.