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Consistent annotation of gene expression arrays

BACKGROUND: Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating the results from the microarray into a biological interpretation requires a...

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Detalles Bibliográficos
Autores principales: Ballester, Benoît, Johnson, Nathan, Proctor, Glenn, Flicek, Paul
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894801/
https://www.ncbi.nlm.nih.gov/pubmed/20459806
http://dx.doi.org/10.1186/1471-2164-11-294
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author Ballester, Benoît
Johnson, Nathan
Proctor, Glenn
Flicek, Paul
author_facet Ballester, Benoît
Johnson, Nathan
Proctor, Glenn
Flicek, Paul
author_sort Ballester, Benoît
collection PubMed
description BACKGROUND: Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases. RESULTS: We have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor. CONCLUSIONS: Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles.
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spelling pubmed-28948012010-07-01 Consistent annotation of gene expression arrays Ballester, Benoît Johnson, Nathan Proctor, Glenn Flicek, Paul BMC Genomics Methodology Article BACKGROUND: Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome. Effectively translating the results from the microarray into a biological interpretation requires an accurate mapping between the probesets on the array and the genes that they are targeting. Although major array manufacturers provide annotations of their gene expression arrays, the methods used by various manufacturers are different and the annotations are difficult to keep up to date in the rapidly changing world of biological sequence databases. RESULTS: We have created a consistent microarray annotation protocol applicable to all of the major array manufacturers. We constantly keep our annotations updated with the latest Ensembl Gene predictions, and thus cross-referenced with a large number of external biomedical sequence database identifiers. We show that these annotations are accurate and address in detail reasons for the minority of probesets that cannot be annotated. Annotations are publicly accessible through the Ensembl Genome Browser and programmatically through the Ensembl Application Programming Interface. They are also seamlessly integrated into the BioMart data-mining tool and the biomaRt package of BioConductor. CONCLUSIONS: Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles. BioMed Central 2010-05-11 /pmc/articles/PMC2894801/ /pubmed/20459806 http://dx.doi.org/10.1186/1471-2164-11-294 Text en Copyright ©2010 Ballester et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Ballester, Benoît
Johnson, Nathan
Proctor, Glenn
Flicek, Paul
Consistent annotation of gene expression arrays
title Consistent annotation of gene expression arrays
title_full Consistent annotation of gene expression arrays
title_fullStr Consistent annotation of gene expression arrays
title_full_unstemmed Consistent annotation of gene expression arrays
title_short Consistent annotation of gene expression arrays
title_sort consistent annotation of gene expression arrays
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894801/
https://www.ncbi.nlm.nih.gov/pubmed/20459806
http://dx.doi.org/10.1186/1471-2164-11-294
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