Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

Tuerei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Oelbei M, Gabor A, Theis F, Korcsmaros T, Saez-Rodriguez J (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Molecular Systems Biology Nature Publishing Group: Open Access Journals - Option B / European Molecular Biology Organization

Book Volume: 17

Article Number: e9923

Journal Issue: 3

DOI: 10.15252/msb.20209923

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.

Involved external institutions

Ruprecht-Karls-Universität Heidelberg DE Germany (DE) Earlham Institute / The Genome Analysis Centre (TGAC) GB United Kingdom (GB) Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE)

How to cite

APA:

Tuerei, D., Valdeolivas, A., Gul, L., Palacio-Escat, N., Klein, M., Ivanova, O.,... Saez-Rodriguez, J. (2021). Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Molecular Systems Biology, 17(3). https://doi.org/10.15252/msb.20209923

MLA:

Tuerei, Denes, et al. "Integrated intra- and intercellular signaling knowledge for multicellular omics analysis." Molecular Systems Biology 17.3 (2021).

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