ArticleNucleic acids research2008
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Should all smokers use combination smoking cessation pharmacotherapy? Using novel analytic methods to detect differential treatment effects over 8 weeks of pharmacotherapy.Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2012Trial
- A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.Nature communications · 2025Article
- A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment.bioRxiv : the preprint server for biology · 2024Article
- Comparison of K-ACS omega · 2019Article
- A systematic evaluation of nucleotide properties for CRISPR sgRNA design.BMC bioinformatics · 2017Article
- Optimization of signal-to-noise ratio for efficient microarray probe design.Bioinformatics (Oxford, England) · 2016Article
- Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays.Sensors (Basel, Switzerland) · 2013Article
- Article
- Correction of spatial bias in oligonucleotide array data.Advances in bioinformatics · 2013Article
- The WalKR system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response.Infection and immunity · 2012Article
- The impact of quantitative optimization of hybridization conditions on gene expression analysis.BMC bioinformatics · 2011Article
- Article
- Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation.Genome research · 2010Article
- A statistical framework for Illumina DNA methylation arrays.Bioinformatics (Oxford, England) · 2010Article
- Tailoring DNA structure to increase target hybridization kinetics on surfaces.Journal of the American Chemical Society · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays.BMC bioinformatics · 2010Article
- Hybridization thermodynamics of NimbleGen microarrays.BMC bioinformatics · 2010Article
- Article
- Direct calibration of PICKY-designed microarrays.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Well-defined relationships between oligonucleotide properties and hybridization signal intensities (HSI) can aid chip design, data normalization and true biological knowledge discovery. We clarify these relationships using the data from two microarray experiments containing over three million probes from 48 high-density chips. We find that melting temperature (T(m)) has the most significant effect on HSI while length for the long oligonucleotides studied has very little effect. Analysis of positional effect using a linear model provides evidence that the protruding ends of probes contribute more than tethered ends to HSI, which is further validated by specifically designed match fragment sliding and extension experiments. The impact of sequence similarity (SeqS) on HSI is not significant in comparison with other oligonucleotide properties. Using regression and regression tree analysis, we prioritize these oligonucleotide properties based on their effects on HSI. The implications of our discoveries for the design of unbiased oligonucleotides are discussed. We propose that isothermal probes designed by varying the length is a viable strategy to reduce sequence bias, though imposing selection constraints on other oligonucleotide properties is also essential.
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