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  Genome wide identification and classification of alternative splicing based on EST data

Gupta, S., Zink, D., Korn, B., Vingron, M., & Haas, S. A. (2004). Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics, 20(16), 2579-2585. doi:10.1093/bioinformatics/bth288.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8863-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8864-F
Genre: Journal Article

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 Creators:
Gupta, Shobhit1, Author
Zink, D., Author
Korn, B., Author
Vingron, Martin2, Author              
Haas, Stefan A.1, Author
Affiliations:
1Max Planck Society, ou_persistent13              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Motivation: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon–intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon–intron boundaries. High quality exon–intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general. Results: Applying the current methodology, constitutive splicing is observed in 33 270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT–PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions.

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Language(s): eng - English
 Dates: 2004-04-29
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 226497
DOI: 10.1093/bioinformatics/bth288
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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 20 (16) Sequence Number: - Start / End Page: 2579 - 2585 Identifier: ISSN: 1367-4803