Expression Profiling Using Affymetrix GeneChip Probe Arrays

Large-scale microarray expression profiling studies have helped us to understand basic biological processes and to classify and predict the prognosis of cancers; they have also accelerated the identification of new drug targets. Affymetrix GeneChip� probe arrays are high-density oligonucleotide microarrays that are available for many prokaryotic and eukaryotic species. Affymetrix human and mouse whole-genome microarrays analyze the expression level of up to 47,000 transcripts and variants. Each transcript is measured by 11 probe pairs, which consist of a perfect match 25mer oligonucleotide (PM) and a 25mer mismatch oligonucleotide (MM) that contains a single base pair mismatch in the central position. The PM/MM design is used for identification and subtraction of nonspecific hybridization and background signals.