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G-spots cause incorrect expression measurement in Affymetrix microarrays

Upton, GJG; Langdon, WB; Harrison, AP; (2008) G-spots cause incorrect expression measurement in Affymetrix microarrays. BMC Genomics , 9 , Article 613. 10.1186/1471-2164-9-613. Green open access

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Abstract

Background: 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. We have tested this expectation by examining the correlations between probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. Results: We have identified probes that are not well-correlated with the other probes in their probeset but nevertheless are highly correlated with probes in other probesets. The common element of these highly correlated probes is that they contain a G-spot (a sequence of four or more guanines). Conclusions: 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.

Type: Article
Title: G-spots cause incorrect expression measurement in Affymetrix microarrays
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2164-9-613
Publisher version: http://dx.doi.org/10.1186/1471-2164-9-613
Language: English
Additional information: © 2008 Upton et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Affymetrix size: 18 pages
Keywords: Microarray, Guanines, G-quadruplex, GEO,
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: http://discovery.ucl.ac.uk/id/eprint/1327710
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