Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
<p>Abstract</p> <p>Background</p> <p>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;...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2007-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/108 |
| _version_ | 1818783165649518592 |
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| author | Cam Margaret C Salit Marc L Lee Joseph C Lu Jun |
| author_facet | Cam Margaret C Salit Marc L Lee Joseph C Lu Jun |
| author_sort | Cam Margaret C |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-18T12:59:52Z |
| format | Article |
| id | doaj.art-4eccb83cb49d4867b666a7d4c0452152 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T12:59:52Z |
| publishDate | 2007-03-01 |
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| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-4eccb83cb49d4867b666a7d4c04521522022-12-21T21:07:10ZengBMCBMC Bioinformatics1471-21052007-03-018110810.1186/1471-2105-8-108Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarraysCam Margaret CSalit Marc LLee Joseph CLu Jun<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/8/108 |
| spellingShingle | Cam Margaret C Salit Marc L Lee Joseph C Lu Jun Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays BMC Bioinformatics |
| 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 |
| url | http://www.biomedcentral.com/1471-2105/8/108 |
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