Standard Article

Using oligonucleotide arrays

Part 2. Genomics

2.8. Expression Profiling

Specialist Review

  1. Lindsay W. Mitchell,
  2. Eric P. Hoffman

Published Online: 15 NOV 2005

DOI: 10.1002/047001153X.g208208

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Mitchell, L. W. and Hoffman, E. P. 2005. Using oligonucleotide arrays. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2:2.8:92.

Author Information

  1. Children's National Medical Center, Washington, DC, USA

Publication History

  1. Published Online: 15 NOV 2005


Nucleic acid sequence microarrays have become one of the first highly parallel, genome-wide technologies to mature into a tool used routinely by biologists in many fields of research. The principle, covered in more detail elsewhere in this volume, is to hybridize a complex solution of labeled mRNA transcripts from cells or tissues onto a solid support containing thousands or millions of segments of unique DNA. The extent of hybridization of each mRNA sequence in the solution to the target “feature” is proportional to the concentration of that specific mRNA in the solution. This “extent of hybridization” to each feature is quantified (signal) by detection tools, which then calculate the relative concentration of the mRNA in the original solution. Affymetrix arrays are factory manufactured microarrays of 25-mer oligonucleotides. Construction of the arrays is accomplished by in situ photochemistry, allowing about 1 million distinct features to be synthesized on 1.2 cM2 quartz supports. The bioinformatics-driven design and production of Affymetrix arrays has made them increasingly popular in both academic and pharmaceutical arenas, and has allowed the development of quality control and standard operating procedures (QC/SOP). This specialist review discusses the design and production of Affymetrix arrays, preparation of target tissue and hybridization, methods of quantifying resulting hybridization data (probe set algorithms), experimental design considerations, and emerging public access databases.


  • expression profiling;
  • mRNA;
  • oligonucleotide;
  • microarray