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Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.
Mol. Syst. Biol. 17:e9923 (2021)
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.
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Publikationstyp
Artikel: Journalartikel
Dokumenttyp
Wissenschaftlicher Artikel
Schlagwörter
Intercellular Signaling ; Ligand-receptor Interactions ; Omics Integration ; Pathways ; Signaling Network
ISSN (print) / ISBN
1744-4292
e-ISSN
1744-4292
Zeitschrift
Molecular Systems Biology
Quellenangaben
Band: 17,
Heft: 3,
Artikelnummer: e9923
Verlag
EMBO Press
Verlagsort
111 River St, Hoboken 07030-5774, Nj Usa
Nichtpatentliteratur
Publikationen
Begutachtungsstatus
Peer reviewed
Institut(e)
Institute of Computational Biology (ICB)
Förderungen
UK Research and Innovation|Biotechnology and Biological Sciences Research Council, Norwich Research Park Biosciences Doctoral Training Partnership grant
UK Research and Innovation|Biotechnology and Biological Sciences Research Council, ISP grant for Gut Microbes and Health
UKRI|Biotechnology and Biological Sciences Research Council (BBSRC)
Deutsche Forschungsgemeinschaft (DFG)
JRC COMBINE, partially funded by Bayer AG
UK Research and Innovation|Biotechnology and Biological Sciences Research Council, ISP grant for Gut Microbes and Health
UKRI|Biotechnology and Biological Sciences Research Council (BBSRC)
Deutsche Forschungsgemeinschaft (DFG)
JRC COMBINE, partially funded by Bayer AG