ArticleComputational biology and chemistry2007
Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.
Article in Computational biology and chemistry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
8 citing papers in PubMed.
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Correction of spatial bias in oligonucleotide array data.Advances in bioinformatics · 2013Article
- ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.BMC bioinformatics · 2011Article
- Application of equilibrium models of solution hybridization to microarray design and analysis.PloS one · 2010Article
- Free energy estimation of short DNA duplex hybridizations.BMC bioinformatics · 2010Article
- Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression.Genetics · 2009Article
- Background correction using dinucleotide affinities improves the performance of GCRMA.BMC bioinformatics · 2008Article
- Design and analysis of mismatch probes for long oligonucleotide microarrays.BMC genomics · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays.
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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.