{"id":24529074,"url":"https://github.com/saezlab/nichenet_omnipath","last_synced_at":"2026-01-02T21:46:52.338Z","repository":{"id":77872851,"uuid":"277854508","full_name":"saezlab/NicheNet_Omnipath","owner":"saezlab","description":"Building and Training of the NicheNet Method exclusively using OmniPath resources. 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For this purpose, it explores the \nmost consistent inter- and intra-cellular protein interactions in accordance \nwith a given gene expression dataset. The authors collected different types of \ninteractions from more than 20 databases to build a ligand-receptor network, a \nsignaling network and a gene regulatory network. OmniPath provides a \nsingle-access point covering all the different types of interactions employed in \nthe NicheNet method. **Therefore, we here highlight the value of OmniPath by \nexclusively using its resources to create a ligand-target regulatory potential \nmodel as described in the NicheNet article** (Browaeys, Saelens and Saeys, 2019).     \n\nNowadays, COVID-19, caused by SARS-CoV-2, is spreading globally throughout the \nplanet. WHO has reported  approximately 10 million confirmed cases and 500 000 \ndeaths to date (June 29, 2020). Against this background, we aim at using our \nOmnipath-based version of NicheNet to explore the autocrine signaling after \nSARS-CoV-2 infection. In particular, **we explore the potential regulatory \neffect of over-expressed ligands after infection on the expression of \ninflammatory response related genes in the Calu3 cell line**. The RNAseq \nexpression data was taken from a recent study. \n\n## Content\n\nThis repository contains the vignettes to reproduce the SARS-CoV-2 case study\npresented in the publication: \n\n\u003e Türei, D., Valdeolivas, A., Gul, L.,  Palacio-Escat, N., Ivanova, O., Modos, D., Korcsmáros T. \u0026 Saez-Rodriguez, J. \nIntegration of intra- and intercellular signaling resources with OmniPath\n\n\n\n## Important Links\n\n### Omnipath:\n\u003chttp://omnipathdb.org/\u003e\n\u003cbr\u003e\n\u003chttps://github.com/saezlab/pypath\u003e\n\u003cbr\u003e\n\u003chttps://saezlab.github.io/OmnipathR/\u003e\n\n### NicheNet:\n\u003chttps://www.nature.com/articles/s41592-019-0667-5\u003e\n\u003cbr\u003e\n\u003chttps://github.com/saeyslab/nichenetr/\u003e\n\n### RNAseq Expression data \n\u003chttps://www.biorxiv.org/content/10.1101/2020.03.24.004655v1\u003e\n\u003cbr\u003e\n\u003chttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147507\u003e\n\n## References\n\n\u003e Türei, D., Korcsmáros, T., \u0026 Saez-Rodriguez, J. (2016). OmniPath: guidelines and gateway for literature-curated signaling pathway resources. _Nature methods_, 13(12), 966–967. [10.1038/nmeth.4077](https://doi.org/10.1038/nmeth.4077)\n\n\u003e Browaeys, R., Saelens, W. \u0026 Saeys, Y. NicheNet: modeling intercellular communication by linking ligands to target genes. _Nature Methods_ 17, 159–162 (2020). [10.1038/s41592-019-0667-5](https://doi.org/10.1038/s41592-019-0667-5)\n\n\u003e Blanco-Melo, D., Nilsson-Payant, B.E., Liu, W.-C., Uhl, S., Hoagland, D., Møller, R., Jordan, T.X., Oishi, K., Panis, M., Sachs, D., Wang, T.T., Schwartz, R.E., Lim, J.K., Albrecht, R.A., tenOever, B.R., 2020. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. _Cell_ 181, 1036–1045.e9. [10.1016/j.cell.2020.04.026](https://doi.org/10.1016/j.cell.2020.04.026)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fnichenet_omnipath","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fnichenet_omnipath","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fnichenet_omnipath/lists"}