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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Nature Portfolio
2021
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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) |
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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 |
work_keys_str_mv |
AT xiaowenchen epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT haithamashoor epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT ryanmusich epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT jiahuiwang epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT mingshengzhang epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT chaozhang epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT mingyanglu epihetforintratumoralepigeneticheterogeneityanalysisandvisualization AT shengli epihetforintratumoralepigeneticheterogeneityanalysisandvisualization |
_version_ |
1718391772183265280 |