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Argelaguet, R.* ; Velten, B.* ; Arnol, D.* ; Dietrich, S.* ; Zenz, T.* ; Marioni, J.C.* ; Buettner, F. ; Huber, W.* ; Stegle, O.*

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Mol. Syst. Biol. 14:e8124 (2018)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Multi‐omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi‐Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi‐omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities. The learnt factors enable a variety of downstream analyses, including identification of sample subgroups, data imputation and the detection of outlier samples. We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profiled for somatic mutations, RNA expression, DNA methylation and ex vivo drug responses. MOFA identified major dimensions of disease heterogeneity, including immunoglobulin heavy‐chain variable region status, trisomy of chromosome 12 and previously underappreciated drivers, such as response to oxidative stress. In a second application, we used MOFA to analyse single‐cell multi‐omics data, identifying coordinated transcriptional and epigenetic changes along cell differentiation.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Data Integration ; Dimensionality Reduction ; Multi-omics ; Personalized Medicine ; Single-cell Omics; Polycyclic Aromatic-hydrocarbons; Lung Epithelial-cells; Yangtze-river Delta; 6 European Cities; Ambient Air; Oxidative Stress; Mouse Lung; A549 Cells; Cytotoxic Responses; Seasonal-variation
ISSN (print) / ISBN 1744-4292
e-ISSN 1744-4292
Zeitschrift Molecular Systems Biology
Quellenangaben Band: 14, Heft: 6, Seiten: , Artikelnummer: e8124 Supplement: ,
Verlag EMBO Press
Verlagsort Po Box 211, 1000 Ae Amsterdam, Netherlands
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)