Hanalyzer Cytoscape Plugins
A number of Cytoscape (http://www.cytoscape.org/) plugins have been developed to aid the user in analyzing the networks produced by the Hanalyzer.
A brief description of each is shown below.
The preferred installation method for all plugins is via the Cytoscape user interface via the Plugins --> Manage Plugins menu.
Alternatively, a compiled distribution as well as source code for each plugin is available to download in the cytoscape-plugins package.
NOTE: If you want to use the Manage Plugins feature you must use Cytoscape v2.6.x.
CommonAttributesThe CommonAttributes plugin [Cytoscape plugin category: Functional Enrichment] allows exploration of provenance and additional information about why two nodes are linked in a Hanalyzer network. Supporting evidence for an interaction is provided via a link to the original journal article(s) asserting the interaction in PubMed when available. Additional evidence links may include the specific web page for an interaction such as a shared annotation term in the Gene Ontology or a shared protein family in Pfam. Further details can be found in (1).
HiderSliderThe HiderSlider plugin [Cytoscape plugin category: Analysis] allows a user to interactively explore a network by hiding/showing nodes or edges with attribute values above an adjustable threshold using a slider bar. Further details can be found in (2).
ReOrientThe ReOrient plugin [Cytoscape plugin category: Analysis] applies node positions from a network in any stored Cytoscape session file to the currently selected network. A network can be created, laid out, and stored with an existing data set. When new data becomes available, a new network can be created and easily compared to the old network by placing nodes in the same positions. Further details can be found in (2).
(1) SM Leach, H Tipney, W Feng, WA Baumgartner Jr, P Kasliwal, RP Schuyler, T Williams, RA Spritz, and L Hunter. Biomedical Discovery Acceleration, with Applications to Craniofacial Development. PLoS Comput Bio 2009, 5(3): e1000215. doi:10.1371/journal.pcbi.1000215 [Link] [PubMed]
(2) H Tipney, RP Schuyler, and L Hunter. Consistent visualizations of changing knowledge. AMIA Summit on Translational Bioinformatics 2009, San Francisco.