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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

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,...

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Main Authors: Türei, Dénes (Author) , Valdeolivas, Alberto (Author) , Gul, Lejla (Author) , Palacio-Escat, Nicolàs (Author) , Klein, Michal (Author) , Ivanova, Olga A. (Author) , Ölbei, Márton (Author) , Gabor, Attila (Author) , Theis, Fabian (Author) , Módos, Dezső (Author) , Korcsmáros, Tamás (Author) , Sáez Rodríguez, Julio (Author)
Format: Article (Journal)
Language:English
Published: 22 March 2021
In: Molecular systems biology
Year: 2021, Volume: 17, Issue: 3, Pages: 1-16
ISSN:1744-4292
DOI:10.15252/msb.20209923
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.15252/msb.20209923
Verlag, kostenfrei, Volltext: https://www.embopress.org/doi/full/10.15252/msb.20209923
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Author Notes:Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian Theis, Dezső Módos, Tamás Korcsmáros &Julio Saez-Rodriguez
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Summary: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.
Item Description:Gesehen am 14.06.2021
Physical Description:Online Resource
ISSN:1744-4292
DOI:10.15252/msb.20209923

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