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G-spots cause incorrect expression measurement in Affymetrix microarrays.

Upton GJ, Langdon WB, Harrison AP - BMC Genomics (2008)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO43SQ, UK. gupton@essex.ac.uk

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. 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.

Results: 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.

Conclusion: 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.

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Heat map illustrating correlation coefficients between every pair of the 16 perfect match probes that form the 31846_at probe set.
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Figure 1: Heat map illustrating correlation coefficients between every pair of the 16 perfect match probes that form the 31846_at probe set.

Mentions: As a visual display of the correlation coefficients between pairs of probes, with the probes selected corresponding to a single exon, we formed "heatmaps" such as that illustrated in Figure 1. In this diagram the shade in each cell represents the value of the correlation coefficient between the values shown by a particular pair of probes. The actual correlation coefficients (multiplied by 10 and rounded) are also shown. The values on the main diagonal are all 10, since the correlation coefficient for a value matched with itself is 1.


G-spots cause incorrect expression measurement in Affymetrix microarrays.

Upton GJ, Langdon WB, Harrison AP - BMC Genomics (2008)

Heat map illustrating correlation coefficients between every pair of the 16 perfect match probes that form the 31846_at probe set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2628396&req=5

Figure 1: Heat map illustrating correlation coefficients between every pair of the 16 perfect match probes that form the 31846_at probe set.
Mentions: As a visual display of the correlation coefficients between pairs of probes, with the probes selected corresponding to a single exon, we formed "heatmaps" such as that illustrated in Figure 1. In this diagram the shade in each cell represents the value of the correlation coefficient between the values shown by a particular pair of probes. The actual correlation coefficients (multiplied by 10 and rounded) are also shown. The values on the main diagonal are all 10, since the correlation coefficient for a value matched with itself is 1.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO43SQ, UK. gupton@essex.ac.uk

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. 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.

Results: 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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus