Analysis of Gene‐Expression Data Using J‐Express

Anne Kristin Stavrum1, Kjell Petersen2, Inge Jonassen2, Bjarte Dysvik3

1 Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway, 2 Computational Biology Unit, BCCS, University of Bergen, Bergen, Norway, 3 MolMine AS, Thormoehlens, Bergen, Norway
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.3
DOI:  10.1002/0471250953.bi0703s21
Online Posting Date:  March, 2008
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The J‐Express package has been designed to facilitate the analysis of microarray data with an emphasis on efficiency, usability, and comprehensibility. The J‐Express system provides a powerful and integrated platform for the analysis of microarray gene expression data. It is platform‐independent in that it requires only the availability of a Java virtual machine on the system. The system includes a range of analysis tools and a project management system supporting the organization and documentation of an analysis project. This unit describes the J‐Express tool, emphasizing central concepts and principles, and gives examples of how it can be used to explore gene expression data sets. Curr. Protoc. Bioinform. 21:7.3.1‐7.3.25. © 2008 by John Wiley & Sons, Inc.

Keywords: gene expression; J‐Express; microarray; spot intensity quantitation

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Table of Contents

  • Introduction
  • Basic Protocol 1: Create a Gene‐Expression Matrix from Spot Intensity Data with J‐Express
  • Basic Protocol 2: Analyze a Gene‐Expression Matrix Using J‐Express
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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