Unit

UNIT 8.7 Using the Reactome Database

  1. Robin Haw,
  2. Lincoln Stein

Published Online: 1 JUN 2012

DOI: 10.1002/0471250953.bi0807s38

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Haw, R. and Stein, L. 2012. Using the Reactome Database. Current Protocols in Bioinformatics. 38:8.7:8.7.1–8.7.23.

Author Information

  1. Ontario Institute for Cancer Research, Toronto, Ontario, Canada

Publication History

  1. Published Online: 1 JUN 2012

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. Curr. Protoc. Bioinform. 38:8.7.1-8.7.23. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • Reactome;
  • reaction;
  • pathway;
  • database;
  • biological pathway;
  • pathway analysis;
  • interaction network;
  • pathway visualization