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. 2012 Jun:Chapter 8:8.7.1-8.7.23.
doi: 10.1002/0471250953.bi0807s38.

Using the reactome database

Robin Haw  1 , Lincoln Stein  1
Affiliations

Using the reactome database

Robin Haw et al. Curr Protoc Bioinformatics. 2012 Jun.

Abstract

There is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center, and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways and processes in the human. It is an expert-authored and peer-reviewed, curated collection of well-documented molecular reactions that span the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm, and other model organisms. This unit describes how to use the Reactome database to learn the steps of a biological pathway; navigate and browse through the Reactome database; identify the pathways in which a molecule of interest is involved; use the Pathway and Expression analysis tools to search the database for and visualize possible connections within user-supplied experimental data set and Reactome pathways; and the Species Comparison tool to compare human and model organism pathways.

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Figures

Figure 8.7.1
Figure 8.7.1
The Reactome home page (www.reactome.org) features a navigation bar and side panel provides access to pathway analysis tools and pathway data.
Figure 8.7.2
Figure 8.7.2
The top-level page describing DNA Repair. The panel to the left contains an expanding hierarchical representation of the current pathway, showing the subpathways that participate in it. The interactive pathway diagram to the right is the main human-readable access point to the Reactome knowledgebase. The details panel below provides further information about the pathway.
Figure 8.7.3
Figure 8.7.3
The Global Genomic NER (GG-NER) subpathway event hierarchy (left), pathway diagram (right) and details panel (bottom). The highlighting in the pathway diagram indicates the reactions involved in this subpathway only.
Figure 8.7.4
Figure 8.7.4
An individual reaction. Notice that the reaction is highlighted by a single green box in the pathway diagram, and that the details panel now shows the constituent input and output molecular compounds that participate in this reaction.
Figure 8.7.5
Figure 8.7.5
After clicking the “Following event(s)” link in the previous figure, the next step in the GG-NER pathway is displayed.
Figure 8.7.6
Figure 8.7.6
This page describes the TFIIH complex. In addition to describing its subunit structure, the details panel displays all the macromolecular complexes and pathways in which TFIIH participates. The context sensitive menu displays all the components of the TFIIH complex.
Figure 8.7.7
Figure 8.7.7
The reference entity page describes the relationship between a molecule as it is represented in Reactome and one or more entries in a third-party database such as UniProt.
Figure 8.7.8
Figure 8.7.8
The context sensitive menu displays the other pathways that the TFIIH complex participates.
Figure 8.7.9
Figure 8.7.9
An interaction overlay of proteins from IntAct that interact with XPA protein.
Figure 8.7.10
Figure 8.7.10
Results from the Cdc7 quick search on the Reactome home page are displayed.
Figure 8.7.11
Figure 8.7.11
The sortable table of results for the “Pathway Assignment” mode of the Reactome Pathway Analysis tool.
Figure 8.7.12
Figure 8.7.12
The results for the “overrepresentation analysis” mode of the Reactome Pathway Analysis tool.
Figure 8.7.13
Figure 8.7.13
The pathway browser displaying the colored physical entities that correspond to gene expression values of experimental data.
Figure 8.7.14
Figure 8.7.14
The pathway browser displaying the results for the comparison of human and mouse Double-Strand Break Repair pathways.
See this image and copyright information in PMC

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