Upton, Graham JG and Langdon, William B and Harrison, Andrew P (2008) G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics, 9 (1). 613-. DOI https://doi.org/10.1186/1471-2164-9-613
Upton, Graham JG and Langdon, William B and Harrison, Andrew P (2008) G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics, 9 (1). 613-. DOI https://doi.org/10.1186/1471-2164-9-613
Upton, Graham JG and Langdon, William B and Harrison, Andrew P (2008) G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics, 9 (1). 613-. DOI https://doi.org/10.1186/1471-2164-9-613
Abstract
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes.</jats:p> </jats:sec>
Item Type: | Article |
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Uncontrolled Keywords: | Guanine; DNA Probes; Oligonucleotide Array Sequence Analysis; Chromosome Mapping; Gene Expression Profiling; Sequence Analysis, DNA; Gene Expression; 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 > Mathematics, Statistics and Actuarial Science, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 30 Sep 2011 10:12 |
Last Modified: | 16 May 2024 17:09 |
URI: | http://repository.essex.ac.uk/id/eprint/830 |
Available files
Filename: 1471-2164-9-613.pdf