Format

Send to

Choose Destination
Curr Protoc Bioinformatics. 2012 Jun;Chapter 8:Unit8.7. doi: 10.1002/0471250953.bi0807s38.

Using the reactome database.

Author information

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

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.

PMID:
22700314
PMCID:
PMC3427849
DOI:
10.1002/0471250953.bi0807s38
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Wiley Icon for PubMed Central
Loading ...
Support Center