Autoren:	Zheng, Zejun Wei, Xiaona Hildebrandt, Andreas Schmidt, Bertil
Titel:	A computational method for studying the relation between alternative splicing and DNA methylation
Online-Publikationsdatum:	13-Okt-2022
Erscheinungsdatum:	2016
Sprache des Dokuments:	Englisch
Zusammenfassung/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.
DDC-Sachgruppe:	570 Biowissenschaften 570 Life sciences
Veröffentlichende Institution:	Johannes Gutenberg-Universität Mainz
Organisationseinheit:	FB 08 Physik, Mathematik u. Informatik
Veröffentlichungsort:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-7983
Version:	Published version
Publikationstyp:	Zeitschriftenaufsatz
Nutzungsrechte:	CC BY
Informationen zu den Nutzungsrechten:	https://creativecommons.org/licenses/by/4.0/
Zeitschrift:	Nucleic acids research 44 2
Seitenzahl oder Artikelnummer:	e19
Verlag:	Oxford Univ. Press
Verlagsort:	Oxford
Erscheinungsdatum:	2016
ISSN:	1362-4962 0305-1048
URL der Originalveröffentlichung:	http://dx.doi.org/10.1093/nar/gkv906
DOI der Originalveröffentlichung:	10.1093/nar/gkv906
Enthalten in den Sammlungen:	DFG-OA-Publizieren (2012 - 2017)