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

Langdon, WB and Upton, GJG and Harrison, AP (2009) 'Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.' Briefings in Bioinformatics, 10 (3). pp. 259-277. ISSN 1467-5463

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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. © The Author 2009. Published by Oxford University Press.

Item Type: Article
Uncontrolled Keywords: Animals; Humans; Guanine; DNA Probes; Oligonucleotide Array Sequence Analysis; Gene Expression Profiling; Nucleic Acid Hybridization; Computational Biology; Biophysics; Molecular Structure; Base Sequence; Nucleic Acid Conformation; Algorithms; Molecular Sequence Data; Databases, Genetic
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health
Faculty of Science and Health > Mathematical Sciences, Department of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 29 Sep 2011 15:24
Last Modified: 15 Jan 2022 00:45

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