A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets
نویسندگان
چکیده
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.
منابع مشابه
An Efficient Covalent Coating on Glass Slides for Preparation of Optical Oligonucleotide Microarrays
Objective(s): Microarrays are potential analyzing tools for genomics and proteomics researches, which is in needed of suitable substrate for coating and also hybridization of biomolecules. Materials and Methods: In this research, a thin film of oxidized agarose was prepared on the glass slides which previously coated with poly-L-lysine (PLL). Some of the aldehyde groups of the activated aga...
متن کاملAssessing Effect of Cross-hybridization on Oligonucleotide Microarrays
We introduce computational method, which allows estimating the input of non-specific binding into hybridization signal intensities on the oligonucleotide-based Affymetrix GeneChip arrays. We consider a simplified linear model of hybridization that should work well for microarray experiments with low DNA concentrations during hybridization, and use the quadratic programming technique to estimate...
متن کاملGlobal gene expression analysis using a zebrafish oligonucleotide microarray platform.
Gene microarray technology permits quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. Gene microarray technology is used in numerous biological disciplines in a variety of applications including global gene expression analysis in relation to developmental stage, to a disease state, and in toxic responses. Herein, we include a demonstration of glo...
متن کاملPosition of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations
A key issue in applications of short oligonucleotide-based microarrays is how to design specific probes with high sensitivity. Some details of the factors affecting microarray hybridization remain unclear, hampering a reliable quantification of target nucleic acids. We have evaluated the effect of the position of the fluorescent label [position of label (POL)] relative to the probe-target duple...
متن کاملEvaluating oligonucleotide properties for DNA microarray probe design
Most current microarray oligonucleotide probe design strategies are based on probe design factors (PDFs), which include probe hybridization free energy (PHFE), probe minimum folding energy (PMFE), dimer score, hairpin score, homology score and complexity score. The impact of these PDFs on probe performance was evaluated using four sets of microarray comparative genome hybridization (aCGH) data,...
متن کامل