CMImpute：跨哺乳动物物种的物种水平DNA甲基化样本的跨物种和组织植入

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-05-20 DOI:10.1186/s13059-025-03561-2

Emily Maciejewski, Steve Horvath, Jason Ernst

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引用次数: 0

摘要

哺乳动物甲基化阵列的大规模应用极大地扩展了哺乳动物物种DNA甲基化数据的可用性。然而，这些数据只捕获了物种组织组合的一小部分。为了解决这个问题，我们开发了CMImpute（跨物种甲基化Imputation），这是一种基于条件变分自编码器的方法，用于计算代表物种组织组合的DNA甲基化。我们证明了CMImpute在输入值和观测值之间实现了很强的样本相关。利用CMImpute和来自348个物种和59种组织类型的数据，我们估算了19,786个新的物种-组织组合的甲基化数据。我们期望CMImpute将成为DNA甲基化分析的有用资源。

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CMImpute: cross-species and tissue imputation of species-level DNA methylation samples across mammalian species

The large-scale application of the mammalian methylation array has substantially expanded the availability of DNA methylation data in mammalian species. However, this data captures only a small portion of species-tissue combinations. To address this, we develop CMImpute (Cross-species Methylation Imputation), a method based on a conditional variational autoencoder, to impute DNA methylation representing species-tissue combinations. We demonstrate that CMImpute achieves strong sample-wise correlation between imputed and observed values. Using CMImpute and data from 348 species and 59 tissue types, we impute methylation data for 19,786 new species-tissue combinations. We expect CMImpute will be a useful resource for DNA methylation analyses.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.