A computational method for studying the relation between alternative splicing and DNA methylation

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
Autoren
Sammlungen
  • metadata
ISSN
1362-4962
Ausgabe der Veröffentlichung
2
Zeitschrift
Nucleic acids research
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Paginierung
e19
Datum der Veröffentlichung
2016
Herausgeber
Oxford Univ. Press
Herausgeber URL
http://dx.doi.org/10.1093/nar/gkv906
Datum der Datenerfassung
2020
Datum, an dem der Datensatz öffentlich gemacht wurde
2020
Zugang
Public
Titel
A computational method for studying the relation between alternative splicing and DNA methylation
Ausgabe der Zeitschrift
44

Datenquelle: METADATA.UB

Andere Metadatenquellen:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000371266000011&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/nar/gkv906
eISSN
1362-4962
Externe Identifier
  • Clarivate Analytics Document Solution ID: DF3RY
  • PubMed Identifier: 26365234
ISSN
0305-1048
Ausgabe der Veröffentlichung
2
Zeitschrift
NUCLEIC ACIDS RESEARCH
Artikelnummer
ARTN e19
Datum der Veröffentlichung
2016
Status
Published
Titel
A computational method for studying the relation between alternative splicing and DNA methylation
Sub types
  • Article
Ausgabe der Zeitschrift
44

Datenquelle: Web of Science (Lite)

Autoren
DOI
10.1093/nar/gkv906
eISSN
1362-4962
ISSN
0305-1048
Ausgabe der Veröffentlichung
2
Zeitschrift
Nucleic Acids Research
Sprache
en
Online publication date
2015
Paginierung
e19 - e19
Datum der Veröffentlichung
2016
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/nar/gkv906
Datum der Datenerfassung
2019
Titel
A computational method for studying the relation between alternative splicing and DNA methylation
Ausgabe der Zeitschrift
44

Datenquelle: Crossref

Abstract
Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation patterns and allows to correlate these patterns with inclusion propensity of exons. Pattern detection is based on dynamic time warping (DTW) of methylation profiles, a sophisticated similarity measure for signals that can be non-trivially transformed. We design a flexible self-organizing map approach to pattern grouping. Exemplary application on available data sets indicates that stable patterns which correlate non-trivially with exon inclusion do indeed exist. To improve the reliability of these predictions, further studies on larger data sets will be required. We have thus taken great care that our software runs efficiently on modern hardware, so that it can support future studies on large-scale data sets.
Addresses
  • Bioinformatics Institute, Singapore 138671, Singapore.
Autoren
DOI
10.1093/nar/gkv906
eISSN
1362-4962
Externe Identifier
  • PubMed Identifier: 26365234
  • PubMed Central ID: PMC4737180
Open access
true
ISSN
0305-1048
Ausgabe der Veröffentlichung
2
Zeitschrift
Nucleic acids research
Schlüsselwörter
  • Humans
  • RNA
  • DNA Methylation
  • Epigenesis, Genetic
  • Alternative Splicing
  • Introns
  • Exons
  • Software
  • Transcriptome
Sprache
eng
Medium
Print-Electronic
Online publication date
2015
Open access status
Open Access
Paginierung
e19
Datum der Veröffentlichung
2016
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2015
Titel
A computational method for studying the relation between alternative splicing and DNA methylation.
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
44

Files

https://academic.oup.com/nar/article-pdf/44/2/e19/17438989/gkv906.pdf https://europepmc.org/articles/PMC4737180?pdf=render

Datenquelle: Europe PubMed Central

Abstract
Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation patterns and allows to correlate these patterns with inclusion propensity of exons. Pattern detection is based on dynamic time warping (DTW) of methylation profiles, a sophisticated similarity measure for signals that can be non-trivially transformed. We design a flexible self-organizing map approach to pattern grouping. Exemplary application on available data sets indicates that stable patterns which correlate non-trivially with exon inclusion do indeed exist. To improve the reliability of these predictions, further studies on larger data sets will be required. We have thus taken great care that our software runs efficiently on modern hardware, so that it can support future studies on large-scale data sets.
Date of acceptance
2015
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/26365234
DOI
10.1093/nar/gkv906
eISSN
1362-4962
Externe Identifier
  • PubMed Central ID: PMC4737180
Ausgabe der Veröffentlichung
2
Zeitschrift
Nucleic Acids Res
Schlüsselwörter
  • Alternative Splicing
  • DNA Methylation
  • Epigenesis, Genetic
  • Exons
  • Humans
  • Introns
  • RNA
  • Software
  • Transcriptome
Sprache
eng
Country
England
Paginierung
e19
PII
gkv906
Datum der Veröffentlichung
2016
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2016
Titel
A computational method for studying the relation between alternative splicing and DNA methylation.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
44

Datenquelle: PubMed

Author's licence
CC-BY
Autoren
Hosting institution
Universitätsbibliothek Mainz
Sammlungen
  • DFG-OA-Publizieren (2012 - 2017)
Resource version
Published version
DOI
10.1093/nar/gkv906
Funding acknowledgements
  • DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin
File(s) embargoed
false
Open access
true
ISSN
1362-4962
Ausgabe der Veröffentlichung
2
Zeitschrift
Nucleic acids research
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Open access status
Open Access
Paginierung
e19
Datum der Veröffentlichung
2016
Public URL
https://openscience.ub.uni-mainz.de/handle/20.500.12030/7998
Herausgeber
Oxford Univ. Press
Herausgeber URL
http://dx.doi.org/10.1093/nar/gkv906
Datum der Datenerfassung
2022
Datum, an dem der Datensatz öffentlich gemacht wurde
2022
Zugang
Public
Titel
A computational method for studying the relation between alternative splicing and DNA methylation
Ausgabe der Zeitschrift
44

Files

a_computational_method_for_st-20220925160254967.pdf

Datenquelle: OPENSCIENCE.UB

Autoren
Zeitschrift
Nucleic acids research
Artikelnummer
2
Paginierung
e19 - e19
Datum der Veröffentlichung
2016
Herausgeber
Oxford University Press
Datum der Datenerfassung
2020
Titel
A computational method for studying the relation between alternative splicing and DNA methylation
Sub types
  • article
Ausgabe der Zeitschrift
44

Datenquelle: Manual

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