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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

View ORCID ProfileDénes Türei, View ORCID ProfileAlberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Olga Ivanova, Attila Gábor, View ORCID ProfileDezső Módos, View ORCID ProfileTamás Korcsmáros, View ORCID ProfileJulio Saez-Rodriguez
doi: https://doi.org/10.1101/2020.08.03.221242
Dénes Türei
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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  • ORCID record for Dénes Türei
Alberto Valdeolivas
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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Lejla Gul
4Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
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Nicolàs Palacio-Escat
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
2RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany
3Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
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Olga Ivanova
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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Attila Gábor
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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Dezső Módos
4Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
5Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
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Tamás Korcsmáros
4Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
5Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
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Julio Saez-Rodriguez
1Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
2RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany
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  • For correspondence: julio.saez@uni-heidelberg.de
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Abstract

Molecular knowledge of biological processes is a cornerstone in the analysis of omics data. Applied to single-cell data, such analyses can provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across different resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources in a single database. It covers the interactions and roles of proteins in inter- and intracellular signal transduction, as well as transcriptional and post-transcriptional regulation. We also provide a comprehensive collection of protein complexes and rich annotations on the properties of proteins, including function, localization, and role in diseases. The resource is available for human, and via homology translation for mouse and rat. The data is accessible via OmniPath’s web service, a Cytoscape plugin, and packages in R/Bioconductor and Python, providing convenient access options for both computational and experimental scientists. Our resource provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications to study SARS-CoV-2 infection and ulcerative colitis.

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Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted August 17, 2020.
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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis
Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Olga Ivanova, Attila Gábor, Dezső Módos, Tamás Korcsmáros, Julio Saez-Rodriguez
bioRxiv 2020.08.03.221242; doi: https://doi.org/10.1101/2020.08.03.221242
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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis
Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Olga Ivanova, Attila Gábor, Dezső Módos, Tamás Korcsmáros, Julio Saez-Rodriguez
bioRxiv 2020.08.03.221242; doi: https://doi.org/10.1101/2020.08.03.221242

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