MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.
MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.
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DOI：
10.1186/s13059-017-1182-6
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发表时间：
2017-03-24
期刊：
影响因子：
12.3
通讯作者：
Walter J
中科院分区：
文献类型：
--
作者：
Lutsik P;Slawski M;Gasparoni G;Vedeneev N;Hein M;Walter J
对于大规模表观基因组研究来说，确定和探索隐藏的混杂变异的性质是很重要的，最重要的是细胞组成。我们开发了MeDeCom作为一种新型的无参考计算框架，允许将复杂的DNA甲基化组分解为潜在的甲基化组分及其在每个样品中的比例。MeDeCom是基于约束非负矩阵分解与一个新的生物动机的正则化函数。它准确地恢复了细胞类型特异性潜在甲基化组分及其比例。MeDeCom是一种新的无监督工具，用于探索性研究甲基化变异的主要来源，这将导致更深入的理解和更好的生物学解释。本文的在线版本（doi：10.1186/s13059-017-1182-6）包含补充材料，可供授权用户使用。
It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation. The online version of this article (doi:10.1186/s13059-017-1182-6) contains supplementary material, which is available to authorized users.