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Identification of protein features encoded by alternative exons using Exon Ontology

Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phe...

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Autores principales: Tranchevent, Léon-Charles, Aubé, Fabien, Dulaurier, Louis, Benoit-Pilven, Clara, Rey, Amandine, Poret, Arnaud, Chautard, Emilie, Mortada, Hussein, Desmet, François-Olivier, Chakrama, Fatima Zahra, Moreno-Garcia, Maira Alejandra, Goillot, Evelyne, Janczarski, Stéphane, Mortreux, Franck, Bourgeois, Cyril F., Auboeuf, Didier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453322/
https://www.ncbi.nlm.nih.gov/pubmed/28420690
http://dx.doi.org/10.1101/gr.212696.116
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author Tranchevent, Léon-Charles
Aubé, Fabien
Dulaurier, Louis
Benoit-Pilven, Clara
Rey, Amandine
Poret, Arnaud
Chautard, Emilie
Mortada, Hussein
Desmet, François-Olivier
Chakrama, Fatima Zahra
Moreno-Garcia, Maira Alejandra
Goillot, Evelyne
Janczarski, Stéphane
Mortreux, Franck
Bourgeois, Cyril F.
Auboeuf, Didier
author_facet Tranchevent, Léon-Charles
Aubé, Fabien
Dulaurier, Louis
Benoit-Pilven, Clara
Rey, Amandine
Poret, Arnaud
Chautard, Emilie
Mortada, Hussein
Desmet, François-Olivier
Chakrama, Fatima Zahra
Moreno-Garcia, Maira Alejandra
Goillot, Evelyne
Janczarski, Stéphane
Mortreux, Franck
Bourgeois, Cyril F.
Auboeuf, Didier
author_sort Tranchevent, Léon-Charles
collection PubMed
description Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.
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spelling pubmed-54533222017-06-15 Identification of protein features encoded by alternative exons using Exon Ontology Tranchevent, Léon-Charles Aubé, Fabien Dulaurier, Louis Benoit-Pilven, Clara Rey, Amandine Poret, Arnaud Chautard, Emilie Mortada, Hussein Desmet, François-Olivier Chakrama, Fatima Zahra Moreno-Garcia, Maira Alejandra Goillot, Evelyne Janczarski, Stéphane Mortreux, Franck Bourgeois, Cyril F. Auboeuf, Didier Genome Res Resource Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. Cold Spring Harbor Laboratory Press 2017-06 /pmc/articles/PMC5453322/ /pubmed/28420690 http://dx.doi.org/10.1101/gr.212696.116 Text en © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Resource
Tranchevent, Léon-Charles
Aubé, Fabien
Dulaurier, Louis
Benoit-Pilven, Clara
Rey, Amandine
Poret, Arnaud
Chautard, Emilie
Mortada, Hussein
Desmet, François-Olivier
Chakrama, Fatima Zahra
Moreno-Garcia, Maira Alejandra
Goillot, Evelyne
Janczarski, Stéphane
Mortreux, Franck
Bourgeois, Cyril F.
Auboeuf, Didier
Identification of protein features encoded by alternative exons using Exon Ontology
title Identification of protein features encoded by alternative exons using Exon Ontology
title_full Identification of protein features encoded by alternative exons using Exon Ontology
title_fullStr Identification of protein features encoded by alternative exons using Exon Ontology
title_full_unstemmed Identification of protein features encoded by alternative exons using Exon Ontology
title_short Identification of protein features encoded by alternative exons using Exon Ontology
title_sort identification of protein features encoded by alternative exons using exon ontology
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453322/
https://www.ncbi.nlm.nih.gov/pubmed/28420690
http://dx.doi.org/10.1101/gr.212696.116
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