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Briefings in Bioinformatics Advance Access originally published online on April 8, 2009
Briefings in Bioinformatics 2009 10(3):259-277; doi:10.1093/bib/bbp018
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips

William B. Langdon, Graham J. G. Upton and Andrew P. Harrison

Corresponding author. Andrew P. Harrison, Department of Mathematical Sciences and Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK. Tel: +44 1206 872964; Fax: +44 1206 873043; E-mail: harry{at}essex.ac.uk

The reliable interpretation of Affymetrix GeneChip data is a multi-faceted problem. The interplay between biophysics, bioinformatics and mining of GeneChip surveys is leading to new insights into how best to analyse the data. Many of the molecular processes occurring on the surfaces of GeneChips result from the high surface density of probes. Interactions between neighbouring adjacent probes affect their rate and strength of hybridization to targets. Competing targets may hybridize to the same probe, and targets may partially bind to more than one probe. The formation of these partial hybrids results in a number of probes not reaching thermodynamic equilibrium during hybridization. Moreover, some targets fold up, or cross-hybridize to other targets. Furthermore, probes may fold and can undergo chemical saturation. There are also sequence-dependent differences in the rates of target desorption during the washing stage. Improvements in the mappings between probe sequence and biological databases are leading to more accurate gene expression profiles. Moreover, algorithms that combine the intensities of multiple probes into single measures of expression are increasingly dependent upon models of the hybridization processes occurring on GeneChips. The large repositories of GeneChip data can be searched for systematic effects across many experiments. This data mining has led to the discovery of a family of thousands of probes, which show correlated expression across thousands of GeneChip experiments. These probes contain runs of guanines, suggesting that G-quadruplexes are able to form on GeneChips. We discuss the impact of these structures on the interpretation of data from GeneChip experiments.

Keywords: Affymetrix Genechips, expression measures, probe correlations, G-quadruplexes

Submitted: December 19, 2008. Received (in revised form): March 3, 2009.


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