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 pathways 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.
[1]
Paul Shannon,et al.
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
,
2015,
F1000Research.
[2]
Guanming Wu,et al.
ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis
,
2014,
F1000Research.
[3]
Guanming Wu.
reactome-fi/CytoscapePlugIn: F1000Research ReactomeFIViz Automation
,
2018
.
[4]
Steven J. M. Jones,et al.
Comprehensive molecular portraits of human breast tumors
,
2012,
Nature.
[5]
L. Stein,et al.
A human functional protein interaction network and its application to cancer data analysis
,
2010,
Genome Biology.
[6]
P. Shannon,et al.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
,
2003,
Genome research.
[7]
Guanming Wu,et al.
reactome-fi/workflows: F1000Research ReactomeFIViz Automation
,
2018
.