New Cytoscape app for functional association network analysis with FunCoup

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Erik Sonnhammer

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Jan 28, 2025, 7:06:14 PMJan 28

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Dear Cytoscape users,

You are welcome to try the new the FunCoup Cytoscape app, which provides a direct interface to all the global functional association networks in the FunCoup database, supporting over 640 species. This app enables researchers to explore gene/protein 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.
Regulatory interactions. FunCoup 6 includes over half a million directed gene regulatory links in the human network, offering insights into transcriptional regulation systems. Another 12 species also contain regulatory links.
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.

See:

"The FunCoup Cytoscape App: multi-species network analysis and visualization"
Davide Buzzao, Lukas Steininger, Dimitri Guala and Erik L.L. Sonnhammer
Bioinformatics, 41:btae739 (2024) [PDF]