Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)

Patrick J. Killion1, Vishwanath R. Iyer1

1 University of Texas at Austin, Austin, Texas
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.10
DOI:  10.1002/0471250953.bi0710s08
Online Posting Date:  December, 2004
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The wide availability and use of DNA microarrays has brought the power of whole‐genome functional characterization to a large variety of research environments. Microarrays, however, also introduce significant infrastructural and analytical concerns with respect to the long‐term warehousing, annotation, and visualization of immense data sets. The Longhorn Array Database (LAD) is a MIAME‐compliant microarray database that operates on PostgreSQL and Linux. It is a free and completely open‐source software solution, and provides a systematic and proven environment in which vast experiment sets can be safely archived, securely accessed, biologically annotated, quantitatively analyzed, and visually explored. This unit provides the complete set of information needed to successfully deploy, configure, and use LAD for the purposes of two‐color DNA microarray analysis and visualization.

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Table of Contents

  • Basic Protocol 1: Database Location and Authentication
  • Basic Protocol 2: Experiment Submission
  • Basic Protocol 3: Experiment Searching
  • Basic Protocol 4: Single‐Experiment Data Analysis
  • Basic Protocol 5: Multiexperiment Data Analysis
  • Support Protocol 1: Synthetically Generate Multiple Experiments for
  • Basic Protocol 6: Manipulating Stored Datasets and Exportable Files
  • Basic Protocol 7: Creating Array Lists
  • Basic Protocol 8: Open Data Publication
  • Guidelines for Understanding Results
  • Commentary
  • Appendix A: User Account Creation
  • Appendix B: Global Resource Creation and Management
  • Appendix C: Installation of the Longhorn Array Database
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
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