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Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays
BACKGROUND: Alternative splicing of exons in a pre-mRNA transcript is an important mechanism which contributes to protein diversity in human. Arrays for detecting alternative splicing are available using several different probe designs, including those based on exon-junctions. In this work, we intro...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631580/ https://www.ncbi.nlm.nih.gov/pubmed/19021909 http://dx.doi.org/10.1186/1471-2164-9-551 |
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author | Kechris, Katerina Yang, Yee Hwa Yeh, Ru-Fang |
author_facet | Kechris, Katerina Yang, Yee Hwa Yeh, Ru-Fang |
author_sort | Kechris, Katerina |
collection | PubMed |
description | BACKGROUND: Alternative splicing of exons in a pre-mRNA transcript is an important mechanism which contributes to protein diversity in human. Arrays for detecting alternative splicing are available using several different probe designs, including those based on exon-junctions. In this work, we introduce a new method for predicting alternatively skipped exons from exon-junction arrays. Predictions based on our method are compared against controls and their sequences are analyzed to identify motifs important for regulating alternative splicing. RESULTS: Our comparison of several alternative methods shows that an exon-skipping score based on neighboring junctions best discriminates between positive and negative controls. Sequence analysis of our predicted exons confirms the presence of known splicing regulatory sequences. In addition, we also derive a set of development-related alternatively spliced genes based on fetal versus adult tissue comparisons and find that our predictions are consistent with their functional annotations. Ab initio motif finding algorithms are applied to identify several motifs that may be relevant for splicing during development. CONCLUSION: This work describes a new method for analyzing exon-junction arrays, identifies sequence motifs that are specific for alternative and constitutive splicing and suggests a role for several known splicing factors and their motifs in developmental regulation. |
format | Text |
id | pubmed-2631580 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26315802009-01-28 Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays Kechris, Katerina Yang, Yee Hwa Yeh, Ru-Fang BMC Genomics Methodology Article BACKGROUND: Alternative splicing of exons in a pre-mRNA transcript is an important mechanism which contributes to protein diversity in human. Arrays for detecting alternative splicing are available using several different probe designs, including those based on exon-junctions. In this work, we introduce a new method for predicting alternatively skipped exons from exon-junction arrays. Predictions based on our method are compared against controls and their sequences are analyzed to identify motifs important for regulating alternative splicing. RESULTS: Our comparison of several alternative methods shows that an exon-skipping score based on neighboring junctions best discriminates between positive and negative controls. Sequence analysis of our predicted exons confirms the presence of known splicing regulatory sequences. In addition, we also derive a set of development-related alternatively spliced genes based on fetal versus adult tissue comparisons and find that our predictions are consistent with their functional annotations. Ab initio motif finding algorithms are applied to identify several motifs that may be relevant for splicing during development. CONCLUSION: This work describes a new method for analyzing exon-junction arrays, identifies sequence motifs that are specific for alternative and constitutive splicing and suggests a role for several known splicing factors and their motifs in developmental regulation. BioMed Central 2008-11-20 /pmc/articles/PMC2631580/ /pubmed/19021909 http://dx.doi.org/10.1186/1471-2164-9-551 Text en Copyright © 2008 Kechris 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 Kechris, Katerina Yang, Yee Hwa Yeh, Ru-Fang Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title | Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title_full | Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title_fullStr | Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title_full_unstemmed | Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title_short | Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
title_sort | prediction of alternatively skipped exons and splicing enhancers from exon junction arrays |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631580/ https://www.ncbi.nlm.nih.gov/pubmed/19021909 http://dx.doi.org/10.1186/1471-2164-9-551 |
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