Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

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.

Authors 9

1. Dénes Türei

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

2. Alberto Valdeolivas

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

3. Lejla Gul

   Norwich Research Park · Earlham Institute

   Affiliation as printed

   Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK

   Earlham Institute, Norwich Research Park, Norwich, NR 7UZ, UK

4. Nicolàs Palacio‐Escat Aachen Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   Heidelberg University · University Hospital Heidelberg · RWTH Aachen University

   Affiliation as printed

   Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

   RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 5074 Aachen, Germany

5. Olga Ivanova

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

6. Attila Gábor

   Heidelberg University · University Hospital Heidelberg

   Affiliation as printed

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

7. Dezső Módos

   Norwich Research Park · Quadram Institute · Earlham Institute

   Affiliation as printed

   Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK

   Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK

   Earlham Institute, Norwich Research Park, Norwich, NR 7UZ, UK

8. Tamas Douglas Korcsmaros

   Norwich Research Park · Quadram Institute · Earlham Institute

   Affiliation as printed

   Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK

   Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK

   Earlham Institute, Norwich Research Park, Norwich, NR 7UZ, UK

9. Julio Sáez-Rodríguez corresponding Aachen Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   Heidelberg University · University Hospital Heidelberg · RWTH Aachen University

   Affiliation as printed

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany

   RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany

   Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 6920 Heidelberg, Germany

   RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 5074 Aachen, Germany