The **FunCoup Cytoscape app** provides a direct interface to [https://funcoup6.scilifelab.se FunCoup] extensive genome-wide functional association networks, supporting over 640 species. This app enables researchers to explore gene interactions and leverage advanced network search algorithms for various biological queries.
Key Features:
- **Comparative interactomics**. Perform cross-species network alignments using orthology data. Two query strategies are available: searching the primary species and mapping to orthologous networks, or querying each species independently. This allows researchers to study conserved interactions across multiple species or focus on species-specific evidence.
- **Advanced network search algorithms**. The app includes several optimized search algorithms:
- *Group search*. Prioritize genes strongly connected to the entire query set.
- *Independent search*. Add interactors for each query gene separately.
- *MaxLink*. Identify direct connections between query and candidate genes using significance tests for disease gene discovery.
- *TOPAS*. A top-down approach that connects query genes within larger disease modules.
- **Human vs SARS-CoV-2 interactome**. Access an extended human interactome including 2,879 links between SARS-CoV-2 and human proteins, aiding in the study of viral-host interactions.
Users can customize and explore networks by filtering based on tissue-specific gene expression or pathway associations, enabling targeted analysis of context-dependent interactions. FunCoup's unique Bayesian integration allows full control over the evidence supporting each link, with detailed information on 10 evidence type and 22 species in the link table.
