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EpiMix: an integrative tool for epigenomic subtyping using DNA methylation

DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been eva...

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Autores principales: Zheng, Yuanning, Jun, John, Brennan, Kevin, Gevaert, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9881910/
https://www.ncbi.nlm.nih.gov/pubmed/36711917
http://dx.doi.org/10.1101/2023.01.03.522660
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author Zheng, Yuanning
Jun, John
Brennan, Kevin
Gevaert, Olivier
author_facet Zheng, Yuanning
Jun, John
Brennan, Kevin
Gevaert, Olivier
author_sort Zheng, Yuanning
collection PubMed
description DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been evaluated to identify differential DNAme present in large and heterogeneous patient cohorts. We developed an end-to-end analytical framework named “EpiMix” for population-level analysis of DNAme and gene expression. Compared to existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. Using cell-type specific data from two separate studies, we discovered novel epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven non-coding RNAs in non-small cell lung cancer.
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spelling pubmed-98819102023-01-28 EpiMix: an integrative tool for epigenomic subtyping using DNA methylation Zheng, Yuanning Jun, John Brennan, Kevin Gevaert, Olivier bioRxiv Article DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been evaluated to identify differential DNAme present in large and heterogeneous patient cohorts. We developed an end-to-end analytical framework named “EpiMix” for population-level analysis of DNAme and gene expression. Compared to existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. Using cell-type specific data from two separate studies, we discovered novel epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven non-coding RNAs in non-small cell lung cancer. Cold Spring Harbor Laboratory 2023-01-04 /pmc/articles/PMC9881910/ /pubmed/36711917 http://dx.doi.org/10.1101/2023.01.03.522660 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Zheng, Yuanning
Jun, John
Brennan, Kevin
Gevaert, Olivier
EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title_full EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title_fullStr EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title_full_unstemmed EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title_short EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
title_sort epimix: an integrative tool for epigenomic subtyping using dna methylation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9881910/
https://www.ncbi.nlm.nih.gov/pubmed/36711917
http://dx.doi.org/10.1101/2023.01.03.522660
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