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Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
Published on: August 10, 2009
G-spots cause incorrect expression measurement in Affymetrix microarrays
Graham Jg Upton1, William B Langdon, Andrew P Harrison
1Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO43SQ, UK. gupton@essex.ac.uk
BMC Genomics
|December 20, 2008
Summary
Probes with G-spots on High Density Oligonucleotide Arrays (HDONAs) show abnormal behavior, correlating poorly with other probes in their set. These untrustworthy probes should be excluded from gene expression analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- High Density Oligonucleotide Arrays (HDONAs) rely on probe sets to measure gene expression.
- Probes containing G-spots (sequences of ≥4 guanines) exhibit anomalous behavior, potentially due to G-quadruplex formation.
Purpose of the Study:
- To investigate the behavior of G-spot probes in HDONAs.
- To determine the impact of G-spots on probe set reliability and gene expression measurements.
Main Methods:
- Analysis of probe correlation coefficients using thousands of arrays from the NCBI Gene Expression Omnibus (GEO) repository.
- Examination of probe behavior based on G-spot location within the probe sequence.
Main Results:
- G-spot probes are poorly correlated with other probes within the same probe set.
- G-spot probes exhibit high correlation with each other, particularly when the G-spot is at the 5' end.
- Over 40% of probe sets on the Affymetrix HG-U133A GeneChip contain at least one G-spot probe.
Conclusions:
- G-spot probes are unreliable for gene expression analysis and should be excluded.
- The high prevalence of G-spot probes impacts the accuracy of existing gene expression data.
- Future HDONA designs should avoid G-spot probes to improve data integrity.
