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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...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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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. |
format | Text |
id | pubmed-2894801 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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