Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data
npj Systems Biology and Applications, vol. 12
Abstract
Single-nuclei transcriptomics enables investigating ligand-receptor mediated cell-cell communication between different cell-types. However, current tools do not allow for non-programmatic means to access this analysis. Additionally, most methods can not account for molecular pathways involved in downstream receptor signaling in cell-cell communication. We developed scVizComm, a ShinyApp based web-portal that can be used to interactively visualize ligand-receptor networks across cell-types and different conditions. scVizComm can be used to host pathway centric pre-calculated cell-cell communication results. Using human kidney and heart single-nuclei transcriptomics data, we showcase the utility of scVizComm in understanding ligand-receptor interactions involved in fibrosis related pathways. Additionally using mouse anterior brain data, we demonstrate the major ligand-receptor expression exploration in space. scVizComm allows interactive visualization and pathway centric prioritization of cell-cell communication analyses.
Authors 4
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Affiliation as printed
Department of Medicine 2, Uniklinik, Aachen, NRW, Germany
Department of Medicine 2, Uniklinik, Pauwelsstraße 30, Aachen, 52074, NRW, Germany
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Institute for Computational Genomics, Uniklinik, Aachen, NRW, Germany
Institute for Computational Genomics, Uniklinik, Pauwelsstraße 30, Pauwelsstraße 30, Aachen, 5074, NRW, Germany
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Affiliation as printed
Department of Medicine 2, Uniklinik, Aachen, NRW, Germany
Department of Medicine 2, Uniklinik, Pauwelsstraße 30, Aachen, 52074, NRW, Germany
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Universitätsklinikum Aachen · Icahn School of Medicine at Mount Sinai
Affiliation as printed
Cardiovascular Research Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. shayat@ukaachen.de
Department of Medicine 2, Uniklinik, Aachen, NRW, Germany. shayat@ukaachen.de
Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA. shayat@ukaachen.de
Department of Medicine 2, Uniklinik, Pauwelsstraße 30, Aachen, 52074, NRW, Germany
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