Multi-omics assessment of dilated cardiomyopathy using non-negative matrix factorization

Rewati Tappu, Jan Haas, David H Lehmann, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Andreas Keller, Hugo A Katus, Norbert Frey and Benjamin Meder

PLOS ONE, 2022, vol. 17, issue 8, 1-26

Abstract: Dilated cardiomyopathy (DCM), a myocardial disease, is heterogeneous and often results in heart failure and sudden cardiac death. Unavailability of cardiac tissue has hindered the comprehensive exploration of gene regulatory networks and nodal players in DCM. In this study, we carried out integrated analysis of transcriptome and methylome data using non-negative matrix factorization from a cohort of DCM patients to uncover underlying latent factors and covarying features between whole-transcriptome and epigenome omics datasets from tissue biopsies of living patients. DNA methylation data from Infinium HM450 and mRNA Illumina sequencing of n = 33 DCM and n = 24 control probands were filtered, analyzed and used as input for matrix factorization using R NMF package. Mann-Whitney U test showed 4 out of 5 latent factors are significantly different between DCM and control probands (P 0.7. Using matrix factorization, multi-omics data derived from human tissue samples can be integrated and novel interactions can be identified. Hypothesis generating nature of such analysis could help to better understand the pathophysiology of complex traits such as DCM.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0272093

DOI: 10.1371/journal.pone.0272093

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