The OmniPath app provides an easy way to import networks from OmniPath web service into Cytoscape. OmniPath is a comprehensive collection of literature curated signaling pathways that, comprising over 50 resources, intended to combine all high quality, manually curated efforts. The web service at [http://omnipathdb.org/ omnipathdb.org] serves five major data sets:
* Signaling pathways (the original OmniPath as described in [https://doi.org/10.1038/nmeth.4077 Turei et al. 2016]);
* Extra kinase-substrate interactions;
* TF Regulons: TF-target gene interactions (as described in [https://doi.org/10.1101/337915 Garcia-Alonso et al. 2018]);
* miRNA-mRNA interactions;
* 57 annotation categories from 32 original resources
With the OmniPath Cytoscape app you can import the data sets above, and fine-tune your custom network by selecting any combinations of the more than 50 resources and filtering the interactions by direction or sign. In addition, the interactions from TF Regulons you can filter them by confidence level (A-D).
We also provide the networks translated to mouse or rat by gene homology.
Please consider the licenses of the original resources. You may find them here: [http://omnipathdb.org/info]
Don’t hesitate to contact us if you have any question regarding the data or you are experiencing issues while using the app: omnipath@googlegroups.com
If you use the tool in a publication, please cite:
Francesco Ceccarelli, Denes Turei, Attila Gabor, Julio Saez-Rodriguez, **Bringing data from curated pathway resources to Cytoscape with OmniPath**, *Bioinformatics*, btz968, [https://doi.org/10.1093/bioinformatics/btz968]
