ArticleBioinformatics (Oxford, England)2008
An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 48 citations in OpenAlex.
- Inference of transcriptome signatures of Escherichia coli in long-term stationary phase.Scientific reports · 2023Article
- The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray.BMC genomics · 2017Article
- Bacterial transcriptome reorganization in thermal adaptive evolution.BMC genomics · 2015Article
- Phenotypic convergence in bacterial adaptive evolution to ethanol stress.BMC evolutionary biology · 2015Article
- Global coordination in adaptation to gene rewiring.Nucleic acids research · 2015Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
- Growth rate-coordinated transcriptome reorganization in bacteria.BMC genomics · 2013Article
- Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.BMC genomics · 2013Article
- Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays.PloS one · 2013Article
- Hybridization and amplification rate correction for affymetrix SNP arrays.BMC medical genomics · 2012Article
- Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli.Molecular systems biology · 2011Article
- Article
- Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.PloS one · 2011Article
- Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.PLoS genetics · 2010Article
- Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.BMC genomics · 2010Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.BMC bioinformatics · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- Hybridization thermodynamics of NimbleGen microarrays.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationHigh-density DNA microarrays provide useful tools to analyze gene expression comprehensively. However, it is still difficult to obtain accurate expression levels from the observed microarray data because the signal intensity is affected by complicated factors involving probe-target hybridization, such as non-linear behavior of hybridization, non-specific hybridization, and folding of probe and target oligonucleotides. Various methods for microarray data analysis have been proposed to address this problem. In our previous report, we presented a benchmark analysis of probe-target hybridization using artificially synthesized oligonucleotides as targets, in which the effect of non-specific hybridization was negligible. The results showed that the preceding models explained the behavior of probe-target hybridization only within a narrow range of target concentrations. More accurate models are required for quantitative expression analysis.
resultsThe experiments showed that finiteness of both probe and target molecules should be considered to explain the hybridization behavior. In this article, we present an extension of the Langmuir model that reproduces the experimental results consistently. In this model, we introduced the effects of secondary structure formation, and dissociation of the probe-target duplex during washing after hybridization. The results will provide useful methods for the understanding and analysis of microarray experiments. AVAILABILITY: The method was implemented for the R software and can be downloaded from our website (http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FHarray/).
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