epihet for intra-tumoral epigenetic heterogeneity analysis and visualization

Abstract Intra-tumoral epigenetic heterogeneity is an indicator of tumor population fitness and is linked to the deregulation of transcription. However, there is no published computational tool to automate the measurement of intra-tumoral epigenetic allelic heterogeneity. We developed an R/Bioconduc...

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Autores principales: Xiaowen Chen, Haitham Ashoor, Ryan Musich, Jiahui Wang, Mingsheng Zhang, Chao Zhang, Mingyang Lu, Sheng Li
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Lenguaje:EN
Publicado: Nature Portfolio 2021
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Acceso en línea:https://doaj.org/article/1a0da502471b4ef1aa309738a04bf2be
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spelling oai:doaj.org-article:1a0da502471b4ef1aa309738a04bf2be2021-12-02T14:12:43Zepihet for intra-tumoral epigenetic heterogeneity analysis and visualization10.1038/s41598-020-79627-x2045-2322https://doaj.org/article/1a0da502471b4ef1aa309738a04bf2be2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79627-xhttps://doaj.org/toc/2045-2322Abstract Intra-tumoral epigenetic heterogeneity is an indicator of tumor population fitness and is linked to the deregulation of transcription. However, there is no published computational tool to automate the measurement of intra-tumoral epigenetic allelic heterogeneity. We developed an R/Bioconductor package, epihet, to calculate the intra-tumoral epigenetic heterogeneity and to perform differential epigenetic heterogeneity analysis. Furthermore, epihet can implement a biological network analysis workflow for transforming cancer-specific differential epigenetic heterogeneity loci into cancer-related biological function and clinical biomarkers. Finally, we demonstrated epihet utility on acute myeloid leukemia. We found statistically significant differential epigenetic heterogeneity (DEH) loci compared to normal controls and constructed co-epigenetic heterogeneity network and modules. epihet is available at https://bioconductor.org/packages/release/bioc/html/epihet.html .Xiaowen ChenHaitham AshoorRyan MusichJiahui WangMingsheng ZhangChao ZhangMingyang LuSheng LiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Xiaowen Chen
Haitham Ashoor
Ryan Musich
Jiahui Wang
Mingsheng Zhang
Chao Zhang
Mingyang Lu
Sheng Li
epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
description Abstract Intra-tumoral epigenetic heterogeneity is an indicator of tumor population fitness and is linked to the deregulation of transcription. However, there is no published computational tool to automate the measurement of intra-tumoral epigenetic allelic heterogeneity. We developed an R/Bioconductor package, epihet, to calculate the intra-tumoral epigenetic heterogeneity and to perform differential epigenetic heterogeneity analysis. Furthermore, epihet can implement a biological network analysis workflow for transforming cancer-specific differential epigenetic heterogeneity loci into cancer-related biological function and clinical biomarkers. Finally, we demonstrated epihet utility on acute myeloid leukemia. We found statistically significant differential epigenetic heterogeneity (DEH) loci compared to normal controls and constructed co-epigenetic heterogeneity network and modules. epihet is available at https://bioconductor.org/packages/release/bioc/html/epihet.html .
format article
author Xiaowen Chen
Haitham Ashoor
Ryan Musich
Jiahui Wang
Mingsheng Zhang
Chao Zhang
Mingyang Lu
Sheng Li
author_facet Xiaowen Chen
Haitham Ashoor
Ryan Musich
Jiahui Wang
Mingsheng Zhang
Chao Zhang
Mingyang Lu
Sheng Li
author_sort Xiaowen Chen
title epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
title_short epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
title_full epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
title_fullStr epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
title_full_unstemmed epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
title_sort epihet for intra-tumoral epigenetic heterogeneity analysis and visualization
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/1a0da502471b4ef1aa309738a04bf2be
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AT mingshengzhang epihetforintratumoralepigeneticheterogeneityanalysisandvisualization
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