Journal
MOLECULAR SYSTEMS BIOLOGY
Volume 17, Issue 3, Pages -Publisher
WILEY
DOI: 10.15252/msb.20209923
Keywords
intercellular signaling; ligand-receptor interactions; omics integration; pathways; signaling network
Categories
Funding
- JRC-COMBINE
- Bayer
- European Union Innovative Medicines Initiative TransQST [116030]
- Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant) [031L0181B]
- DFG (Deutsche Forschungsgemeinschaft/German Research Council) [SA 3554/1-2]
- Earlham Institute (Norwich, UK)
- Quadram Institute (Norwich, UK)
- UKRI Biotechnological and Biosciences Research Council (BBSRC) UK [BB/J004529/1, BB/P016774/1, BB/CSP17270/1]
- BBSRC ISP grant for Gut Microbes and Health [BB/R012490/1, BBS/E/F/000PR10353, BBS/E/F/000PR10355]
- BBSRC Norwich Research Park Biosciences Doctoral Training Partnership grant [BB/M011216/1]
- Projekt DEAL
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Molecular knowledge of biological processes is crucial for omics data analysis, with OmniPath providing a comprehensive resource for researchers to access information on both intracellular and intercellular processes. This resource facilitates the study of cell-cell interactions and downstream signaling processes, demonstrated in applications investigating SARS-CoV-2 infection and ulcerative colitis.
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 (), 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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