Automation of ReactomeFIViz via CyREST API

Fred Loney, Guanming Wu
2018 F1000Research  
Pathway-and network-based approaches project seemingly unrelated genes onto the context of pathways and networks, enhancing the analysis power that cannot be achieved via gene-based approaches. Pathway and network approaches are routinely applied in large-scale data analysis for cancer and other complicated diseases. ReactomeFIViz is a Cytoscape app, providing features for researchers to perform pathway-and network-based data analysis and visualization by leveraging manually curated Reactome
more » ... hways and highly reliable Reactome functional interaction network. To facilitate adoption of this app in bioinformatics software pipeline and workflow development, we develop a CyREST API for ReactomeFIViz by exposing some major features in the app. We describe a use case to demonstrate the use of this API in a Python-based notebook, and believe the new API will provide the community a convenient and powerful tool to perform pathway-and network-based data analysis and visualization using our app in an automatic way. PubMed Abstract | Publisher Full Text | Free Full Text 2. Ono K, Muetze T, Kolishovski G, et al.: CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API [version 1; referees: 2 approved]. F1000Res. 2015; 4: 478. PubMed Abstract | Publisher Full Text | Free Full Text 3. Fabregat A, Jupe S, Matthews L, et al.: The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018; 46(D1): D649-D655. PubMed Abstract | Publisher Full Text | Free Full Text 4. Wu G, Feng X, Stein L: A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010; 11(5): R53. PubMed Abstract | Publisher Full Text | Free Full Text 5. Wu G, Dawson E, Duong A, et al.: ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis [version 2; referees: 2 approved]. F1000Res. 2014; 3: 146. PubMed Abstract | Publisher Full Text | Free Full Text 6. Cancer Genome Atlas Network: Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490(7418): 61-70. PubMed Abstract | Publisher Full Text | Free Full Text
doi:10.12688/f1000research.14776.1 pmid:29946442 pmcid:PMC5998009 fatcat:l2y2r3trdzayxeyb75fcjcosve