Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Molecular Systems Biology, vol. 17, pp. e9923
Abstract
Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter- and intracellular signaling, as well as transcriptional and post-transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via OmniPath's web service (https://omnipathdb.org/), a Cytoscape plug-in, and packages in R/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell-cell interactions and affected downstream intracellular signaling processes. OmniPath provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications studying SARS-CoV-2 infection and ulcerative colitis.
Authors 12
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Heidelberg University · University Hospital Heidelberg
Affiliation as printed
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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Heidelberg University · University Hospital Heidelberg
Affiliation as printed
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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Affiliation as printed
Earlham Institute, Norwich, UK
Earlham Institute Norwich UK
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Nicolàs Palacio‐Escat Aachen Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE) Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE)
Heidelberg University · University Hospital Heidelberg · RWTH Aachen University
Affiliation as printed
Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
Faculty of Biosciences Heidelberg University Heidelberg Germany
Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE) RWTH Aachen University Aachen Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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Helmholtz Munich · Institute of Computational Biology
Affiliation as printed
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
Institute of Computational Biology Helmholtz Zentrum München Neuherberg Germany
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Heidelberg University · University Hospital Heidelberg
Affiliation as printed
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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Quadram Institute · Earlham Institute
Affiliation as printed
Earlham Institute, Norwich, UK
Quadram Institute Bioscience, Norwich, UK
Earlham Institute Norwich UK
Quadram Institute Bioscience Norwich UK
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Heidelberg University · University Hospital Heidelberg
Affiliation as printed
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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Helmholtz Munich · Institute of Computational Biology · Technical University of Munich
Affiliation as printed
Department of Mathematics, Technical University of Munich, Garching, Germany
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
Department of Mathematics Technical University of Munich Garching Germany
Institute of Computational Biology Helmholtz Zentrum München Neuherberg Germany
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Quadram Institute · Earlham Institute
Affiliation as printed
Earlham Institute, Norwich, UK
Quadram Institute Bioscience, Norwich, UK
Earlham Institute Norwich UK
Quadram Institute Bioscience Norwich UK
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Quadram Institute · Earlham Institute
Affiliation as printed
Earlham Institute, Norwich, UK
Quadram Institute Bioscience, Norwich, UK
Earlham Institute Norwich UK
Quadram Institute Bioscience Norwich UK
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Julio Sáez-Rodríguez corresponding Aachen Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE) Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE)
Heidelberg University · University Hospital Heidelberg · RWTH Aachen University
Affiliation as printed
Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE) RWTH Aachen University Aachen Germany
Faculty of Medicine and Heidelberg University Hospital Institute of Computational Biomedicine Heidelberg University Heidelberg Germany
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