Cargando…
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
BACKGROUND: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions f...
Autores principales: | , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2007
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853115/ https://www.ncbi.nlm.nih.gov/pubmed/17394657 http://dx.doi.org/10.1186/1471-2105-8-108 |
_version_ | 1782133111467802624 |
---|---|
author | Lu, Jun Lee, Joseph C Salit, Marc L Cam, Margaret C |
author_facet | Lu, Jun Lee, Joseph C Salit, Marc L Cam, Margaret C |
author_sort | Lu, Jun |
collection | PubMed |
description | BACKGROUND: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis. RESULTS: Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. CONCLUSION: We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software. |
format | Text |
id | pubmed-1853115 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-18531152007-04-20 Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays Lu, Jun Lee, Joseph C Salit, Marc L Cam, Margaret C BMC Bioinformatics Methodology Article BACKGROUND: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis. RESULTS: Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. CONCLUSION: We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software. BioMed Central 2007-03-29 /pmc/articles/PMC1853115/ /pubmed/17394657 http://dx.doi.org/10.1186/1471-2105-8-108 Text en Copyright © 2007 Lu 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 Lu, Jun Lee, Joseph C Salit, Marc L Cam, Margaret C Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title_full | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title_fullStr | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title_full_unstemmed | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title_short | Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays |
title_sort | transcript-based redefinition of grouped oligonucleotide probe sets using aceview: high-resolution annotation for microarrays |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853115/ https://www.ncbi.nlm.nih.gov/pubmed/17394657 http://dx.doi.org/10.1186/1471-2105-8-108 |
work_keys_str_mv | AT lujun transcriptbasedredefinitionofgroupedoligonucleotideprobesetsusingaceviewhighresolutionannotationformicroarrays AT leejosephc transcriptbasedredefinitionofgroupedoligonucleotideprobesetsusingaceviewhighresolutionannotationformicroarrays AT salitmarcl transcriptbasedredefinitionofgroupedoligonucleotideprobesetsusingaceviewhighresolutionannotationformicroarrays AT cammargaretc transcriptbasedredefinitionofgroupedoligonucleotideprobesetsusingaceviewhighresolutionannotationformicroarrays |