MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

Authors:
Open Access
Publisher website
Google Scholar
Abstract
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.
Funding Information
  • EU 7th Framework Programme (267038 (NOTOX))
  • Deutsche Forschungsgemeinschaft (Cluster of Excellence MMCI)
  • Bundesministerium für Forschung, Technologie und Raumfahrt (01KU1216A (DEEP))

This publication has 64 references indexed in Scilit: