Cargando…
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...
Autores principales: | , |
---|---|
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 |
_version_ | 1782124772467933184 |
---|---|
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. |
format | Text |
id | pubmed-1188054 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT pereziratxetacarolina inconsistenciesovertimein5ofnetaffxprobetogeneannotations AT andrademiguela inconsistenciesovertimein5ofnetaffxprobetogeneannotations |