Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies

Proportion of cancerous cells in a tumor sample, known as "tumor purity", is a major source of confounding factor in cancer data analyses. Lots of computational methods are available for estimating tumor purity from different types of genomics data or based on different platforms, which ma...

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Autores principales:	Nana Wei, Hanwen Zhu, Chun Li, Xiaoqi Zheng
Formato:	article
Lenguaje:	EN
Publicado:	AIMS Press 2021
Materias:	tumor purity differential methylation tumor sample clustering dna methylation analysis webserver Biotechnology TP248.13-248.65 Mathematics QA1-939
Acceso en línea:	https://doaj.org/article/40351e5ffa674548b5f05bd56ff7f17d
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spelling	oai:doaj.org-article:40351e5ffa674548b5f05bd56ff7f17d2021-11-29T02:49:09ZPurimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies10.3934/mbe.20214411551-0018https://doaj.org/article/40351e5ffa674548b5f05bd56ff7f17d2021-10-01T00:00:00Zhttps://www.aimspress.com/article/doi/10.3934/mbe.2021441?viewType=HTMLhttps://doaj.org/toc/1551-0018Proportion of cancerous cells in a tumor sample, known as "tumor purity", is a major source of confounding factor in cancer data analyses. Lots of computational methods are available for estimating tumor purity from different types of genomics data or based on different platforms, which makes it difficult to compare and integrate the estimated results. To rectify the deviation caused by tumor purity effect, a number of methods for downstream data analysis have been developed, including tumor sample clustering, association study and differential methylation between tumor samples. However, using these computational tools remains a daunting task for many researchers since they require non-trivial computational skills. To this end, we present Purimeth, an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies. Purimeth implements three state-of-the-art methods for tumor purity estimation from DNA methylation array data: InfiniumPurify, MEpurity and PAMES. It also provides graphical interface for various analyses including differential methylation (DM), sample clustering, and purification of tumor methylomes, all with the consideration of tumor purities. In addition, Purimeth catalogs estimated tumor purities for TCGA samples from nine methods for users to visualize and explore. In conclusion, Purimeth provides an easy-operated way for researchers to explore tumor purity and implement cancer methylation data analysis. It is developed using Shiny (Version 1.6.0) and freely available at http://purimeth.comp-epi.com/.Nana WeiHanwen Zhu Chun Li Xiaoqi ZhengAIMS Pressarticletumor puritydifferential methylationtumor sample clusteringdna methylation analysiswebserverBiotechnologyTP248.13-248.65MathematicsQA1-939ENMathematical Biosciences and Engineering, Vol 18, Iss 6, Pp 8951-8961 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	tumor purity differential methylation tumor sample clustering dna methylation analysis webserver Biotechnology TP248.13-248.65 Mathematics QA1-939
spellingShingle	tumor purity differential methylation tumor sample clustering dna methylation analysis webserver Biotechnology TP248.13-248.65 Mathematics QA1-939 Nana Wei Hanwen Zhu Chun Li Xiaoqi Zheng Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
description	Proportion of cancerous cells in a tumor sample, known as "tumor purity", is a major source of confounding factor in cancer data analyses. Lots of computational methods are available for estimating tumor purity from different types of genomics data or based on different platforms, which makes it difficult to compare and integrate the estimated results. To rectify the deviation caused by tumor purity effect, a number of methods for downstream data analysis have been developed, including tumor sample clustering, association study and differential methylation between tumor samples. However, using these computational tools remains a daunting task for many researchers since they require non-trivial computational skills. To this end, we present Purimeth, an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies. Purimeth implements three state-of-the-art methods for tumor purity estimation from DNA methylation array data: InfiniumPurify, MEpurity and PAMES. It also provides graphical interface for various analyses including differential methylation (DM), sample clustering, and purification of tumor methylomes, all with the consideration of tumor purities. In addition, Purimeth catalogs estimated tumor purities for TCGA samples from nine methods for users to visualize and explore. In conclusion, Purimeth provides an easy-operated way for researchers to explore tumor purity and implement cancer methylation data analysis. It is developed using Shiny (Version 1.6.0) and freely available at http://purimeth.comp-epi.com/.
format	article
author	Nana Wei Hanwen Zhu Chun Li Xiaoqi Zheng
author_facet	Nana Wei Hanwen Zhu Chun Li Xiaoqi Zheng
author_sort	Nana Wei
title	Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
title_short	Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
title_full	Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
title_fullStr	Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
title_full_unstemmed	Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies
title_sort	purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer dna methylation studies
publisher	AIMS Press
publishDate	2021
url	https://doaj.org/article/40351e5ffa674548b5f05bd56ff7f17d
work_keys_str_mv	AT nanawei purimethanintegratedwebbasedtoolforestimatingandaccountingfortumorpurityincancerdnamethylationstudies AT hanwenzhu purimethanintegratedwebbasedtoolforestimatingandaccountingfortumorpurityincancerdnamethylationstudies AT chunli purimethanintegratedwebbasedtoolforestimatingandaccountingfortumorpurityincancerdnamethylationstudies AT xiaoqizheng purimethanintegratedwebbasedtoolforestimatingandaccountingfortumorpurityincancerdnamethylationstudies
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Purimeth: an integrated web-based tool for estimating and accounting for tumor purity in cancer DNA methylation studies

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