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Improving comparability between microarray probe signals by thermodynamic intensity correction

Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between differen...

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Autores principales: Bruun, Georg M., Wernersson, Rasmus, Juncker, Agnieszka S., Willenbrock, Hanni, Nielsen, Henrik Bjørn
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1874658/
https://www.ncbi.nlm.nih.gov/pubmed/17337437
http://dx.doi.org/10.1093/nar/gkl1098
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author Bruun, Georg M.
Wernersson, Rasmus
Juncker, Agnieszka S.
Willenbrock, Hanni
Nielsen, Henrik Bjørn
author_facet Bruun, Georg M.
Wernersson, Rasmus
Juncker, Agnieszka S.
Willenbrock, Hanni
Nielsen, Henrik Bjørn
author_sort Bruun, Georg M.
collection PubMed
description Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between different probes. It is therefore of great interest to correct for the variation between probes. Much of this variation is sequence dependent. We demonstrate that a thermodynamic model for hybridization of either DNA or RNA to a DNA microarray, which takes the sequence-dependent probe affinities into account significantly reduces the signal fluctuation between probes targeting the same gene transcript. For a test set of tightly tiled yeast genes, the model reduces the variance by up to a factor ∼1/3. As a consequence of this reduction, the model is shown to yield a more accurate determination of transcription start sites for a subset of yeast genes. In another application, we identify present/absent calls for probes hybridized to the sequenced Escherichia coli strain O157:H7 EDL933. The model improves the correct calls from 85 to 95% relative to raw intensity measures. The model thus makes applications which depend on comparisons between probes aimed at different sections of the same target more reliable.
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spelling pubmed-18746582007-05-25 Improving comparability between microarray probe signals by thermodynamic intensity correction Bruun, Georg M. Wernersson, Rasmus Juncker, Agnieszka S. Willenbrock, Hanni Nielsen, Henrik Bjørn Nucleic Acids Res Methods Online Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between different probes. It is therefore of great interest to correct for the variation between probes. Much of this variation is sequence dependent. We demonstrate that a thermodynamic model for hybridization of either DNA or RNA to a DNA microarray, which takes the sequence-dependent probe affinities into account significantly reduces the signal fluctuation between probes targeting the same gene transcript. For a test set of tightly tiled yeast genes, the model reduces the variance by up to a factor ∼1/3. As a consequence of this reduction, the model is shown to yield a more accurate determination of transcription start sites for a subset of yeast genes. In another application, we identify present/absent calls for probes hybridized to the sequenced Escherichia coli strain O157:H7 EDL933. The model improves the correct calls from 85 to 95% relative to raw intensity measures. The model thus makes applications which depend on comparisons between probes aimed at different sections of the same target more reliable. Oxford University Press 2007-04 2007-03-02 /pmc/articles/PMC1874658/ /pubmed/17337437 http://dx.doi.org/10.1093/nar/gkl1098 Text en © 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Bruun, Georg M.
Wernersson, Rasmus
Juncker, Agnieszka S.
Willenbrock, Hanni
Nielsen, Henrik Bjørn
Improving comparability between microarray probe signals by thermodynamic intensity correction
title Improving comparability between microarray probe signals by thermodynamic intensity correction
title_full Improving comparability between microarray probe signals by thermodynamic intensity correction
title_fullStr Improving comparability between microarray probe signals by thermodynamic intensity correction
title_full_unstemmed Improving comparability between microarray probe signals by thermodynamic intensity correction
title_short Improving comparability between microarray probe signals by thermodynamic intensity correction
title_sort improving comparability between microarray probe signals by thermodynamic intensity correction
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1874658/
https://www.ncbi.nlm.nih.gov/pubmed/17337437
http://dx.doi.org/10.1093/nar/gkl1098
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