scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract The increasing availability of single-cell multi-omics data allows to quantitatively characterize gene regulation. We here describe scMEGA (Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference) to infer gene regulatory networks by combining single-cell gene expression and chromatin accessibility profiles. This enables to study of complex gene regulation mechanisms for dynamic biological processes, such as cellular differentiation and disease-driven cellular remodeling. We provide a case study on gene regulatory networks controlling myofibroblast activation in human myocardial infarction

Authors 5

1. Zhijian Li Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52062 Aachen, Germany

2. James Shiniti Nagai Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52062 Aachen, Germany

3. Christoph Kuppe Aachen Division of Nephrology and Clinical Immunology Institute of Experimental Medicine and Systems Biology

   RWTH Aachen University

   Affiliation as printed

   Division of Nephrology and Clinical Immunology, RWTH Aachen University, 52062 Aachen, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, 52062 Aachen, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, 506 Aachen, Germany

4. Rafael Kramann Aachen Division of Nephrology and Clinical Immunology Institute of Experimental Medicine and Systems Biology

   Erasmus MC · RWTH Aachen University

   Affiliation as printed

   Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, Netherlands

   Division of Nephrology and Clinical Immunology, RWTH Aachen University, 52062 Aachen, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, 52062 Aachen, Germany

   Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, 506 Aachen, Germany

5. Ivan G. Costa corresponding Aachen Institute for Computational Genomics Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   RWTH Aachen University

   Affiliation as printed

   Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52062 Aachen, Germany