Data Storage and Analysis in ArrayExpress and Expression Profiler

Gabriella Rustici1, Misha Kapushesky1, Nikolay Kolesnikov1, Helen Parkinson1, Ugis Sarkans1, Alvis Brazma1

1 European Bioinformatics Institute (EMBL‐EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.13
DOI:  10.1002/0471250953.bi0713s23
Online Posting Date:  September, 2008
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ArrayExpress at the European Bioinformatics Institute is a public database for MIAME‐compliant microarray and transcriptomics data. It consists of two parts: the ArrayExpress Repository, which is a public archive of microarray data, and the ArrayExpress Warehouse of Gene Expression Profiles, which contains additionally curated subsets of data from the Repository. Archived experiments can be queried by experimental attributes, such as keywords, species, array platform, publication details, or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms, allowing expression profiles visualization. The data can be exported and analyzed using the online data analysis tool named Expression Profiler. Data analysis components, such as data preprocessing, filtering, differentially expressed gene finding, clustering methods, and ordination‐based techniques, as well as other statistical tools are all available in Expression Profiler, via integration with the statistical package R. Curr. Protoc. Bioinform. 23:7.13.1‐7.13.27. © 2008 by John Wiley & Sons, Inc.

Keywords: gene expression; microarrays; transcriptomics; public repository; data analysis

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Table of Contents

  • Introduction
  • Basic Protocol 1: Querying Gene Expression Profiles
  • Basic Protocol 2: Query the AE Repository of Microarray and Transcriptomics Data
  • Basic Protocol 3: How to Upload, Normalize, Analyze, and Visualize Data in Expression Profiler
  • Basic Protocol 4: How to Perform Clustering Analysis in Expression Profiler
  • Basic Protocol 5: How to Calculate Gene Ontology Term Enrichment in Expression Profiler
  • Basic Protocol 6: How to Calculate Chromosome Co‐Localization Probability in Expression Profiler
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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