Overview of mRNA Expression Profiling Using DNA Microarrays

Fumiaki Katagiri1, Jane Glazebrook1

1 University of Minnesota, St. Paul, Minnesota
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 22.4
DOI:  10.1002/0471142727.mb2204s85
Online Posting Date:  January, 2009
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DNA microarray technology allows simultaneous measurement of the mRNA levels of thousands of genes. This powerful technology has applications in addressing many biological questions that were not approachable previously; however, the enormous size of microarray data sets leads to issues of experimental design and statistical analysis that are unfamiliar to many molecular biologists. The type of array used, the design of the biological experiment, the number of experimental replicates, and the statistical method for data analysis should all be chosen based on the scientific goals of the investigator. This overview presents a discussion of the relative merits and limitations of various methods with respect to some common applications of microarray experiments. Curr. Protoc. Mol. Biol. 85:22.4.1‐22.4.13. © 2009 by John Wiley & Sons, Inc.

Keywords: oligonucleotide arrays; statistical analysis; significance tests; false discovery rate; transcriptome profiling

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Table of Contents

  • Introduction
  • Advantages and Limitations of mRNA Profiling
  • Probes Used in DNA Microarray
  • Two‐Channel and Single‐Channel Methods
  • DNA Microarray Technologies
  • Analysis of mRNA Profile Data
  • Preprocessing: Conversion of Scanned Array Images to Expression Level Values
  • Inferential Statistics Used in Discovery of Differentially Expressed Genes
  • Obtaining Software for Microarray Data Analysis
  • Acknowledgment
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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