Using the Reactome database

Curr Protoc Bioinformatics. 2004 Oct;Chapter 8:Unit 8.7. doi: 10.1002/0471250953.bi0807s7.

Abstract

There is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between Cold Spring Harbor Laboratory and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways in the human. It is a curated collection of well-documented molecular reactions that span the gamut from simple intermediate metabolism to complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, and other model organisms. This unit describes how to use the Reactome database to learn the steps of a biological pathway and see how one pathway interacts with another; navigate and browse through the Reactome database; identify the pathways in which a molecule of interest is involved; use the Pathfinder tool to search the database for possible connections within and between pathways.

MeSH terms

  • Databases, Protein*
  • Gene Expression Profiling / methods*
  • Information Storage and Retrieval / methods*
  • Protein Interaction Mapping / methods*
  • Proteome / classification
  • Proteome / metabolism*
  • Signal Transduction / physiology*
  • User-Computer Interface*

Substances

  • Proteome