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Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets
BACKGROUND: The function and significance of the widespread expression of natural antisense transcripts (NATs) is largely unknown. The ability to quantitatively assess changes in NAT expression for many different transcripts in multiple samples would facilitate our understanding of this relatively n...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929078/ https://www.ncbi.nlm.nih.gov/pubmed/17598913 http://dx.doi.org/10.1186/1471-2164-8-200 |
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author | Oeder, Sebastian Mages, Joerg Flicek, Paul Lang, Roland |
author_facet | Oeder, Sebastian Mages, Joerg Flicek, Paul Lang, Roland |
author_sort | Oeder, Sebastian |
collection | PubMed |
description | BACKGROUND: The function and significance of the widespread expression of natural antisense transcripts (NATs) is largely unknown. The ability to quantitatively assess changes in NAT expression for many different transcripts in multiple samples would facilitate our understanding of this relatively new class of RNA molecules. RESULTS: Here, we demonstrate that standard expression analysis Affymetrix MOE430 and HG-U133 GeneChips contain hundreds of probe sets that detect NATs. Probe sets carrying a "Negative Strand Matching Probes" annotation in NetAffx were validated using Ensembl by manual and automated approaches. More than 50 % of the 1,113 probe sets with "Negative Strand Matching Probes" on the MOE430 2.0 GeneChip were confirmed as detecting NATs. Expression of selected antisense transcripts as indicated by Affymetrix data was confirmed using strand-specific RT-PCR. Thus, Affymetrix datasets can be mined to reveal information about the regulated expression of a considerable number of NATs. In a correlation analysis of 179 sense-antisense (SAS) probe set pairs using publicly available data from 1637 MOE430 2.0 GeneChips a significant number of SAS transcript pairs were found to be positively correlated. CONCLUSION: Standard expression analysis Affymetrix GeneChips can be used to measure many different NATs. The large amount of samples deposited in microarray databases represents a valuable resource for a quantitative analysis of NAT expression and regulation in different cells, tissues and biological conditions. |
format | Text |
id | pubmed-1929078 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-19290782007-07-21 Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets Oeder, Sebastian Mages, Joerg Flicek, Paul Lang, Roland BMC Genomics Research Article BACKGROUND: The function and significance of the widespread expression of natural antisense transcripts (NATs) is largely unknown. The ability to quantitatively assess changes in NAT expression for many different transcripts in multiple samples would facilitate our understanding of this relatively new class of RNA molecules. RESULTS: Here, we demonstrate that standard expression analysis Affymetrix MOE430 and HG-U133 GeneChips contain hundreds of probe sets that detect NATs. Probe sets carrying a "Negative Strand Matching Probes" annotation in NetAffx were validated using Ensembl by manual and automated approaches. More than 50 % of the 1,113 probe sets with "Negative Strand Matching Probes" on the MOE430 2.0 GeneChip were confirmed as detecting NATs. Expression of selected antisense transcripts as indicated by Affymetrix data was confirmed using strand-specific RT-PCR. Thus, Affymetrix datasets can be mined to reveal information about the regulated expression of a considerable number of NATs. In a correlation analysis of 179 sense-antisense (SAS) probe set pairs using publicly available data from 1637 MOE430 2.0 GeneChips a significant number of SAS transcript pairs were found to be positively correlated. CONCLUSION: Standard expression analysis Affymetrix GeneChips can be used to measure many different NATs. The large amount of samples deposited in microarray databases represents a valuable resource for a quantitative analysis of NAT expression and regulation in different cells, tissues and biological conditions. BioMed Central 2007-06-28 /pmc/articles/PMC1929078/ /pubmed/17598913 http://dx.doi.org/10.1186/1471-2164-8-200 Text en Copyright © 2007 Oeder 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 | Research Article Oeder, Sebastian Mages, Joerg Flicek, Paul Lang, Roland Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title_full | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title_fullStr | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title_full_unstemmed | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title_short | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
title_sort | uncovering information on expression of natural antisense transcripts in affymetrix moe430 datasets |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929078/ https://www.ncbi.nlm.nih.gov/pubmed/17598913 http://dx.doi.org/10.1186/1471-2164-8-200 |
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