MersV1, Main, Exploration, bibRecord, 001C27

Identifying splicing regulatory elements with de Bruijn graphs.

Identifieur interne : 001C27 ( Main/Exploration ); précédent : 001C26; suivant : 001C28

Identifying splicing regulatory elements with de Bruijn graphs.

Auteurs : Eman Badr [États-Unis] ; Lenwood S. Heath

Source :

Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2014.

RBID : pubmed:25393830

Descripteurs français

KwdFr :
- Biologie informatique, Exons (génétique), Génome, Humains, Introns, Séquence nucléotidique, Séquences d'acides nucléiques régulatrices (génétique), Épissage alternatif (génétique), Épissage des ARN (génétique).
MESH :
- génétique : Exons, Séquences d'acides nucléiques régulatrices, Épissage alternatif, Épissage des ARN.
- Biologie informatique, Génome, Humains, Introns, Séquence nucléotidique.

English descriptors

KwdEn :
- Alternative Splicing (genetics), Base Sequence, Computational Biology, Exons (genetics), Genome, Humans, Introns, RNA Splicing (genetics), Regulatory Sequences, Nucleic Acid (genetics).
MESH :
- genetics : Alternative Splicing, Exons, RNA Splicing, Regulatory Sequences, Nucleic Acid.
- Base Sequence, Computational Biology, Genome, Humans, Introns.

Abstract

Splicing regulatory elements (SREs) are short, degenerate sequences on pre-mRNA molecules that enhance or inhibit the splicing process via the binding of splicing factors, proteins that regulate the functioning of the spliceosome. Existing methods for identifying SREs in a genome are either experimental or computational. Here, we propose a formalism based on de Bruijn graphs that combines genomic structure, word count enrichment analysis, and experimental evidence to identify SREs found in exons. In our approach, SREs are not restricted to a fixed length (i.e., k-mers, for a fixed k). As a result, we identify 2001 putative exonic enhancers and 3080 putative exonic silencers for human genes, with lengths varying from 6 to 15 nucleotides. Many of the predicted SREs overlap with experimentally verified binding sites. Our model provides a novel method to predict variable length putative regulatory elements computationally for further experimental investigation.

DOI: 10.1089/cmb.2014.0183
PubMed: 25393830

Affiliations:

Le document en format XML

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<wicri:cityArea>Department of Computer Science, Virginia Tech , Blacksburg</wicri:cityArea>
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<term>Genome</term>
<term>Humans</term>
<term>Introns</term>
<term>RNA Splicing (genetics)</term>
<term>Regulatory Sequences, Nucleic Acid (genetics)</term>
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<term>Exons (génétique)</term>
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<term>Introns</term>
<term>Séquence nucléotidique</term>
<term>Séquences d'acides nucléiques régulatrices (génétique)</term>
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<term>Épissage des ARN (génétique)</term>
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<term>Regulatory Sequences, Nucleic Acid</term>
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<term>Séquences d'acides nucléiques régulatrices</term>
<term>Épissage alternatif</term>
<term>Épissage des ARN</term>
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<term>Computational Biology</term>
<term>Genome</term>
<term>Humans</term>
<term>Introns</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term>
<term>Génome</term>
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<front><div type="abstract" xml:lang="en">Splicing regulatory elements (SREs) are short, degenerate sequences on pre-mRNA molecules that enhance or inhibit the splicing process via the binding of splicing factors, proteins that regulate the functioning of the spliceosome. Existing methods for identifying SREs in a genome are either experimental or computational. Here, we propose a formalism based on de Bruijn graphs that combines genomic structure, word count enrichment analysis, and experimental evidence to identify SREs found in exons. In our approach, SREs are not restricted to a fixed length (i.e., k-mers, for a fixed k). As a result, we identify 2001 putative exonic enhancers and 3080 putative exonic silencers for human genes, with lengths varying from 6 to 15 nucleotides. Many of the predicted SREs overlap with experimentally verified binding sites. Our model provides a novel method to predict variable length putative regulatory elements computationally for further experimental investigation.</div>
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Serveur d'exploration MERS

Identifying splicing regulatory elements with de Bruijn graphs.

Identifying splicing regulatory elements with de Bruijn graphs.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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