Nature Biotechnology21, 818 - 821 (2003)
Published online: 8 June 2003; | doi:10.1038/nbt836
There is a Corrigenda (August 2003) associated with this Letters.
A model of molecular interactions on short oligonucleotide
microarrays
Li Zhang1, Michael F Miles2
& Kenneth D Aldape3
1
Department of Biostatistics, The University of
Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd.
447, Houston, Texas 77030,
USA.
2
Departments of Pharmacology/Toxicology and
Neurology and the Center for Study of Biological Complexity, Virginia
Commonwealth University, Richmond, Virginia
23298-0599, USA.
3
Department of Pathology & Brain Tumor Center,
The University of Texas M.D. Anderson Cancer Center, 1515
Holcombe Blvd. 447, Houston, Texas
77030, USA.
High-density short oligonucleotide microarrays have become a widely
used tool for measuring gene expression on a large scale1,
2.
However, details of the mechanism of binding on microarrays remain unclear3. Short oligonucleotide probes currently synthesized on microarrays
are often ineffective as a result of limited sequence specificity or low
sensitivity. Here, we describe a model of binding interactions on microarrays
that reveals how probe signals depend on probe sequences and why certain probes
are ineffective. The model indicates that the amount of nonspecific binding can
be estimated from a simple rule. Using this model, we have developed an
improved measure of gene expression for use in data analysis.
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