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Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction

Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integrat...

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Autores principales: Taguchi, Y-h., Komaki, Shohei, Sutoh, Yoichi, Ohmomo, Hideki, Otsuka-Yamasaki, Yayoi, Shimizu, Atsushi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411815/
https://www.ncbi.nlm.nih.gov/pubmed/37556429
http://dx.doi.org/10.1371/journal.pone.0289029
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author Taguchi, Y-h.
Komaki, Shohei
Sutoh, Yoichi
Ohmomo, Hideki
Otsuka-Yamasaki, Yayoi
Shimizu, Atsushi
author_facet Taguchi, Y-h.
Komaki, Shohei
Sutoh, Yoichi
Ohmomo, Hideki
Otsuka-Yamasaki, Yayoi
Shimizu, Atsushi
author_sort Taguchi, Y-h.
collection PubMed
description Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integration of pairwise coincidences) is difficult. In this study, we integrated gene expression, DNA methylation, and genome variants from the iMETHYL database using the recently proposed kernel tensor decomposition-based unsupervised feature extraction method with limited computational resources (i.e., short CPU time and small memory requirements). Our methods do not require prior knowledge of the subjects because they are fully unsupervised in that unsupervised tensor decomposition is used. The selected genes and genomic variants were significantly targeted by transcription factors that were biologically enriched in KEGG pathway terms as well as in the intra-related regulatory network. The proposed method is promising for integrated analyses of gene expression, methylation, and genomic variants with limited computational resources.
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spelling pubmed-104118152023-08-10 Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction Taguchi, Y-h. Komaki, Shohei Sutoh, Yoichi Ohmomo, Hideki Otsuka-Yamasaki, Yayoi Shimizu, Atsushi PLoS One Research Article Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integration of pairwise coincidences) is difficult. In this study, we integrated gene expression, DNA methylation, and genome variants from the iMETHYL database using the recently proposed kernel tensor decomposition-based unsupervised feature extraction method with limited computational resources (i.e., short CPU time and small memory requirements). Our methods do not require prior knowledge of the subjects because they are fully unsupervised in that unsupervised tensor decomposition is used. The selected genes and genomic variants were significantly targeted by transcription factors that were biologically enriched in KEGG pathway terms as well as in the intra-related regulatory network. The proposed method is promising for integrated analyses of gene expression, methylation, and genomic variants with limited computational resources. Public Library of Science 2023-08-09 /pmc/articles/PMC10411815/ /pubmed/37556429 http://dx.doi.org/10.1371/journal.pone.0289029 Text en © 2023 Taguchi et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Taguchi, Y-h.
Komaki, Shohei
Sutoh, Yoichi
Ohmomo, Hideki
Otsuka-Yamasaki, Yayoi
Shimizu, Atsushi
Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title_full Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title_fullStr Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title_full_unstemmed Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title_short Integrated analysis of human DNA methylation, gene expression, and genomic variation in iMETHYL database using kernel tensor decomposition-based unsupervised feature extraction
title_sort integrated analysis of human dna methylation, gene expression, and genomic variation in imethyl database using kernel tensor decomposition-based unsupervised feature extraction
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10411815/
https://www.ncbi.nlm.nih.gov/pubmed/37556429
http://dx.doi.org/10.1371/journal.pone.0289029
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