Usersguide - ReactomeWiki http://wiki.reactome.org/index.

php/Usersguide

Usersguide
Contents
1 Introduction
2 What is Reactome?
3 The Reactome Front Page
3.1 The Navigation Bar
3.2 The Six Tool Buttons
3.3 The Main Text
4 The Pathway Browser and Tools
4.1 The Pathway Browser
4.1.1 The Pathway Hierarchy Panel
4.1.2 Pathway Diagrams
4.1.3 Navigating Pathway Diagrams
4.1.3.1 Sub-pathway Diagrams
4.1.4 Details Panel
4.1.4.1 Pathway Details Panel
4.1.4.2 Reaction Details Panel
4.1.4.3 Protein, Small Molecule, Complex and Set Details
4.1.5 Context Sensitive Menus in Pathway Diagrams
4.1.5.1 Right-click Menu Items associated with Pathway Nodes
4.1.5.2 Right-click Menu Items associated with Pathway Diagram
4.1.5.3 Pathway Options Menu
4.1.6 Navigating Disease Pathway Diagrams
4.1.7 View Equivalent Pathway In Another Species
4.1.8 Molecular Interaction Overlay
4.1.8.1 MI Overlay tab
4.1.8.2 Search Pathway Diagram
5 Searching Reactome
5.1 Simple searches
5.2 Advanced Search
5.3 Small Molecule Search Tool
5.4 Author/Reviewer Search Tool
6 Reactome Tools
6.1 Pathway Analysis
6.1.1 Gene list Dataset
6.1.2 Dataset from a Model Organism
6.1.2.1 "Project to Human" Pathway Analysis
6.1.2.2 "Computationally Inferred Non-Human" Pathway Analysis
6.1.3 Expression Analysis
6.2 Species Comparison
6.3 FI Network Tool
6.3.1 Overview
6.3.2 Download and Launch the Reactome FI plugin
6.3.3 Use Reactome Pathways
6.3.3.1 Explore Reactome Pathways
6.3.3.2 Display Reactome Pathways in the FI Network View
6.3.3.3 Pathway Enrichment Analysis
6.3.3.4 Probabilistic Graphical Model based Pathway Analysis
6.3.4 Use the Reactome Functional Interaction (FI) Network
6.3.4.1 Gene Set/Mutation Analysis
6.3.4.2 HotNet Mutation Analysis
6.3.4.3 Microarray Data Analysis
6.3.5 Other Features Related to the FI Network
6.3.5.1 Query FI Source
6.3.5.2 Fetch FIs for Node
6.3.5.3 Show Pathway Diagram
6.3.5.4 Load Cancer Gene Index Annotations
6.3.5.5 Survival Analysis
7 Download Reactome
8 Exporting Data From Reactome

Introduction
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
(mailto:help@reactome.org) 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

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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.

Reactome Home Page

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.

The Navigation Bar

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.

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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:

Browse Pathw ays

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

Pathway Browser

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 (http://www.reactome.org/pages/documentation/electronically-inferred-events/)). 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.

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Analyse Data Opens a panel where analyses can be performed

Quick Tour click here for a short introduction to Reactomes 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.

The 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 Hierarchy

Pathway Hierarchy Symbols

Pathway Diagrams
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.

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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.

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