***Note that the CyThesaurus plugin is also required, version 1.3.1 or higher:***
**[http://apps.cytoscape.org/apps/cythesaurusidmapping >>> Download CyThesaurus]**
Unique among overrepresentation analysis tools, the Network Ontology Analysis (NOA) plugin not only annotates and analyzes the nodes in your network, but also can take the network connectivity of annotated nodes into account. Based on the NOA algorithm ([http://nar.oxfordjournals.org/content/39/13/e87.long Wang, et. al, 2011]), the network edges are annotated using a combination of ontology terms found on the connected nodes. This approach produces better results than just treating the networks as an annotated gene list in a number of cases. The NOA plugin can also perform traditional overrepresentation analysis for standard cases and direct comparison of approaches with your data.
The NOA plugin also takes care of annotating your network with Gene Ontology terms. Just select from the provided ontology files and indicate a node attribute with a standard identifier, then you are ready to perform the analysis.
The NOA plugin also supports batch mode, where you can perform simultaneous analysis of multiple networks. The results are provided in standard tables and as a heatmap for batch mode. These data can be exported to your favorite third-party tool for custom visualization and further analysis.