Expression Data Analysis with Reactome

Steve Jupe1, Antonio Fabregat1, Henning Hermjakob1

1 European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.20
DOI:  10.1002/0471250953.bi0820s49
Online Posting Date:  March, 2015
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Abstract

The Reactome database of curated biological pathways provides a tool for visualizing user‐supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and determine whether all that are necessary are present. Several experiments can be visualized in succession, to determine whether expression changes with experimental conditions, a useful feature for examining a time‐course, dose‐response, or disease progression. © 2015 by John Wiley & Sons, Inc.

Keywords: reactome; pathway; expression analysis; microarray; quantitative proteomics

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using the Analyze Data Tool with Expression Data
  • Commentary
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Haw, R. and Stein, L. 2012. Using the reactome database. Curr. Protoc. Bioinform. 38:8.7:8.7.1‐8.7.23.
  Jamison, D. C. 2003. Structured query language (SQL) fundamentals. Curr. Protoc. Bioinform. 00:9.2:9.2.1‐9.2.29.
Internet Resources
  http://www.biopax.org
  BioPAX: Biological Pathways Exchange. Standardizing the file format for representing biological pathways.
  http://www.reactome.org
  The Reactome home page.
  http://www.sbml.org
  SBML: Systems Biology Markup Language. Standardizing the file format for representing models of biological pathways.
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