ArticleBMC genomics2008
G-spots cause incorrect expression measurement in Affymetrix microarrays.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed.
- G-spot: Fact or Fiction?: A Systematic Review.Sexual medicine · 2021Review
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Optimization of signal-to-noise ratio for efficient microarray probe design.Bioinformatics (Oxford, England) · 2016Article
- Article
- Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data.Microarrays (Basel, Switzerland) · 2014Article
- Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays.Sensors (Basel, Switzerland) · 2013Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression.PloS one · 2013Article
- Does the G-spot exist? A review of the current literature.International urogynecology journal · 2012Review
- Motif effects in Affymetrix GeneChips seriously affect probe intensities.Nucleic acids research · 2012Article
- The LO-BaFL method and ALS microarray expression analysis.BMC bioinformatics · 2012Article
- Normalized Affymetrix expression data are biased by G-quadruplex formation.Nucleic acids research · 2012Article
- ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.BMC bioinformatics · 2011Article
- A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach.Computer physics communications · 2010Article
- A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia.Journal of nucleic acids · 2010Article
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.BMC bioinformatics · 2010Article
- Detection call algorithms for high-throughput gene expression microarray data.Briefings in bioinformatics · 2010Review
- Article
- Evolving DNA motifs to predict GeneChip probe performance.Algorithms for molecular biology : AMB · 2009Article
- Correlating measurements across samples improves accuracy of large-scale expression profile experiments.Genome biology · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundHigh 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.
resultsWe 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.
conclusionSince 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.