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Estimation of data-specific constitutive exons with RNA-Seq data
BACKGROUND: RNA-Seq has the potential to answer many diverse and interesting questions about the inner workings of cells. Estimating changes in the overall transcription of a gene is not straightforward. Changes in overall gene transcription can easily be confounded with changes in exon usage which...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656776/ https://www.ncbi.nlm.nih.gov/pubmed/23360225 http://dx.doi.org/10.1186/1471-2105-14-31 |
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author | Patrick, Ellis Buckley, Michael Yang, Yee Hwa |
author_facet | Patrick, Ellis Buckley, Michael Yang, Yee Hwa |
author_sort | Patrick, Ellis |
collection | PubMed |
description | BACKGROUND: RNA-Seq has the potential to answer many diverse and interesting questions about the inner workings of cells. Estimating changes in the overall transcription of a gene is not straightforward. Changes in overall gene transcription can easily be confounded with changes in exon usage which alter the lengths of transcripts produced by a gene. Measuring the expression of constitutive exons— exons which are consistently conserved after splicing— offers an unbiased estimation of the overall transcription of a gene. RESULTS: We propose a clustering-based method, exClust, for estimating the exons that are consistently conserved after splicing in a given data set. These are considered as the exons which are “constitutive” in this data. The method utilises information from both annotation and the dataset of interest. The method is implemented in an openly available R function package, sydSeq. CONCLUSION: When used on two real datasets exClust includes more than three times as many reads as the standard UI method, and improves concordance with qRT-PCR data. When compared to other methods, our method is shown to produce robust estimates of overall gene transcription. |
format | Online Article Text |
id | pubmed-3656776 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36567762013-05-20 Estimation of data-specific constitutive exons with RNA-Seq data Patrick, Ellis Buckley, Michael Yang, Yee Hwa BMC Bioinformatics Methodology Article BACKGROUND: RNA-Seq has the potential to answer many diverse and interesting questions about the inner workings of cells. Estimating changes in the overall transcription of a gene is not straightforward. Changes in overall gene transcription can easily be confounded with changes in exon usage which alter the lengths of transcripts produced by a gene. Measuring the expression of constitutive exons— exons which are consistently conserved after splicing— offers an unbiased estimation of the overall transcription of a gene. RESULTS: We propose a clustering-based method, exClust, for estimating the exons that are consistently conserved after splicing in a given data set. These are considered as the exons which are “constitutive” in this data. The method utilises information from both annotation and the dataset of interest. The method is implemented in an openly available R function package, sydSeq. CONCLUSION: When used on two real datasets exClust includes more than three times as many reads as the standard UI method, and improves concordance with qRT-PCR data. When compared to other methods, our method is shown to produce robust estimates of overall gene transcription. BioMed Central 2013-01-29 /pmc/articles/PMC3656776/ /pubmed/23360225 http://dx.doi.org/10.1186/1471-2105-14-31 Text en Copyright © 2013 Patrick 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 Patrick, Ellis Buckley, Michael Yang, Yee Hwa Estimation of data-specific constitutive exons with RNA-Seq data |
title | Estimation of data-specific constitutive exons with RNA-Seq data |
title_full | Estimation of data-specific constitutive exons with RNA-Seq data |
title_fullStr | Estimation of data-specific constitutive exons with RNA-Seq data |
title_full_unstemmed | Estimation of data-specific constitutive exons with RNA-Seq data |
title_short | Estimation of data-specific constitutive exons with RNA-Seq data |
title_sort | estimation of data-specific constitutive exons with rna-seq data |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656776/ https://www.ncbi.nlm.nih.gov/pubmed/23360225 http://dx.doi.org/10.1186/1471-2105-14-31 |
work_keys_str_mv | AT patrickellis estimationofdataspecificconstitutiveexonswithrnaseqdata AT buckleymichael estimationofdataspecificconstitutiveexonswithrnaseqdata AT yangyeehwa estimationofdataspecificconstitutiveexonswithrnaseqdata |