Introduction

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.

Publications

  1. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.
    Cite this
    Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J, 2017-03-01 - Genome biology

Credits

  1. Pavlo Lutsik
    Developer

    Present address: Division of Cancer Epigenetics, German Cancer Research Center, Germany

  2. Martin Slawski
    Developer

    Present address: Department of Statistics, Volgenau School of Engineering, United States of America

  3. Gilles Gasparoni
    Developer

    Department of EpiGenetics, Saarland University, Germany

  4. Nikita Vedeneev
    Developer

    Machine Learning Group, Saarland University, Germany

  5. Matthias Hein
    Developer

    Machine Learning Group, Saarland University, Germany

  6. Jörn Walter
    Investigator

    Department of EpiGenetics, Saarland University, Germany

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Summary
AccessionBT000823
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByJörn Walter