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Inconsistencies over time in 5% of NetAffx probe-to-gene annotations

BACKGROUND: DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations between probes and genes can change as the sequence data are updated. However, it is frequent that the report...

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Detalles Bibliográficos
Autores principales: Perez-Iratxeta, Carolina, Andrade, Miguel A
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188054/
https://www.ncbi.nlm.nih.gov/pubmed/16033654
http://dx.doi.org/10.1186/1471-2105-6-183
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author Perez-Iratxeta, Carolina
Andrade, Miguel A
author_facet Perez-Iratxeta, Carolina
Andrade, Miguel A
author_sort Perez-Iratxeta, Carolina
collection PubMed
description BACKGROUND: DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations between probes and genes can change as the sequence data are updated. However, it is frequent that the reported results of microarray analyses are given just as lists of genes without any reference to the underlying probes. RESULTS: We show for a particular commercial microarray design that the number of probes associated to some genes change with time. These changes concern approximately 5% of the probe sets across the history of annotation releases over a two year span. CONCLUSION: We recommend to report probe set identifiers when publishing microarray results, and to submit those analyses to microarray public databases to ensure that the interpretation of the data is updated with the latest set of annotations.
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spelling pubmed-11880542005-08-20 Inconsistencies over time in 5% of NetAffx probe-to-gene annotations Perez-Iratxeta, Carolina Andrade, Miguel A BMC Bioinformatics Correspondence BACKGROUND: DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations between probes and genes can change as the sequence data are updated. However, it is frequent that the reported results of microarray analyses are given just as lists of genes without any reference to the underlying probes. RESULTS: We show for a particular commercial microarray design that the number of probes associated to some genes change with time. These changes concern approximately 5% of the probe sets across the history of annotation releases over a two year span. CONCLUSION: We recommend to report probe set identifiers when publishing microarray results, and to submit those analyses to microarray public databases to ensure that the interpretation of the data is updated with the latest set of annotations. BioMed Central 2005-07-20 /pmc/articles/PMC1188054/ /pubmed/16033654 http://dx.doi.org/10.1186/1471-2105-6-183 Text en Copyright © 2005 Perez-Iratxeta and Andrade; 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 Correspondence
Perez-Iratxeta, Carolina
Andrade, Miguel A
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title_full Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title_fullStr Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title_full_unstemmed Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title_short Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
title_sort inconsistencies over time in 5% of netaffx probe-to-gene annotations
topic Correspondence
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188054/
https://www.ncbi.nlm.nih.gov/pubmed/16033654
http://dx.doi.org/10.1186/1471-2105-6-183
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