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Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning
Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722613/ https://www.ncbi.nlm.nih.gov/pubmed/31374967 http://dx.doi.org/10.3390/genes10080587 |
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author | Louadi, Zakaria Oubounyt, Mhaned Tayara, Hilal Chong, Kil To |
author_facet | Louadi, Zakaria Oubounyt, Mhaned Tayara, Hilal Chong, Kil To |
author_sort | Louadi, Zakaria |
collection | PubMed |
description | Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as “Splicing Codes”. The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5’ss, alternative 3’ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method. |
format | Online Article Text |
id | pubmed-6722613 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-67226132019-09-10 Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning Louadi, Zakaria Oubounyt, Mhaned Tayara, Hilal Chong, Kil To Genes (Basel) Article Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as “Splicing Codes”. The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5’ss, alternative 3’ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method. MDPI 2019-08-01 /pmc/articles/PMC6722613/ /pubmed/31374967 http://dx.doi.org/10.3390/genes10080587 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Louadi, Zakaria Oubounyt, Mhaned Tayara, Hilal Chong, Kil To Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title | Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title_full | Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title_fullStr | Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title_full_unstemmed | Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title_short | Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning |
title_sort | deep splicing code: classifying alternative splicing events using deep learning |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722613/ https://www.ncbi.nlm.nih.gov/pubmed/31374967 http://dx.doi.org/10.3390/genes10080587 |
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